From 95ad3e6c89b8c45d0efb70505c30f0303f5b0ca8 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Thu, 8 Oct 2026 22:59:02 +0200 Subject: [PATCH 01/44] fix: exclude lumped pool and artificial reactions from the balance test (#1153) A reaction in the "Pool reactions" or "Artificial reactions" subsystem stands for many species at once, so an elemental balance is not defined for it. Both subsystems join the boundary and biomass exclusions that balanceTest.py already applies, which drops 44 rows from the report (42 mass, 12 charge, overlapping) and leaves 178. R and X stay elements of their own rather than being ignored, so a reaction using them is still expected to balance in them. --- code/test/balanceTest.py | 28 ++++++++++++++-- code/test/unit/test_balance_test.py | 52 +++++++++++++++++++++++++++++ data/testResults/README.md | 4 ++- 3 files changed, 80 insertions(+), 4 deletions(-) create mode 100644 code/test/unit/test_balance_test.py diff --git a/code/test/balanceTest.py b/code/test/balanceTest.py index 27cc7344d..318dea905 100644 --- a/code/test/balanceTest.py +++ b/code/test/balanceTest.py @@ -3,8 +3,16 @@ Uses cobrapy's Reaction.check_mass_balance(), which reports both elemental (mass) and charge imbalances in a single call. Boundary reactions -(exchange/demand/sink) and the biomass reaction are excluded, since they are -not expected to balance. +(exchange/demand/sink), the biomass reaction and the lumped reactions of the +"Pool reactions" and "Artificial reactions" subsystems are excluded, since they +are not expected to balance: a pool reaction stands for many species at once +and carries fractional coefficients against the R pseudo-element, and an +artificial conversion lumps a whole class of metabolites into one pool. + +R and X are left as elements of their own, not ignored. A reaction that uses +them is still expected to balance in them, and several do not: the +"[protein] to [protein]-L-" reactions are off by one X and two R, +which is a finding rather than noise (#1153). The unbalanced reactions are written, sorted, to data/testResults/balance_results.csv, so that a pull request introducing a new @@ -17,6 +25,18 @@ import cobra +# A reaction in one of these subsystems lumps many species into a single +# pseudo-reaction, so an elemental balance is not defined for it. +LUMPED_SUBSYSTEMS = frozenset({"Pool reactions", "Artificial reactions"}) + + +def _subsystems(rxn): + """A reaction's subsystems as a set; the YAML gives either a list or a string.""" + sub = rxn.subsystem + if isinstance(sub, (list, tuple, set)): + return {str(s) for s in sub} + return {str(sub)} if sub else set() + def main(): model = cobra.io.load_yaml_model("model/Human-GEM.yml") @@ -27,6 +47,8 @@ def main(): continue if "biomass" in rxn.id.lower() or "biomass" in (rxn.name or "").lower(): continue + if _subsystems(rxn) & LUMPED_SUBSYSTEMS: + continue try: imbalance = rxn.check_mass_balance() except Exception as exc: # noqa: BLE001 - record, do not silently drop @@ -53,7 +75,7 @@ def main(): n_mass = sum(1 for r in rows if r[2]) # includes uncheckable reactions (surfaced, not hidden) n_charge = sum(1 for r in rows if r[3]) print( - f"Unbalanced reactions (excluding boundary and biomass): {len(rows)} " + f"Unbalanced reactions (excluding boundary, biomass and lumped): {len(rows)} " f"({n_mass} mass, {n_charge} charge, {len(errored)} could not be checked)" ) if errored: diff --git a/code/test/unit/test_balance_test.py b/code/test/unit/test_balance_test.py new file mode 100644 index 000000000..4616f6865 --- /dev/null +++ b/code/test/unit/test_balance_test.py @@ -0,0 +1,52 @@ +"""balanceTest skips the lumped reactions, and keeps R and X as elements.""" + +import cobra +import pytest + +import balanceTest + + +def _rxn(rid, mets, subsystem=None): + rxn = cobra.Reaction(rid, lower_bound=0, upper_bound=1000) + rxn.add_metabolites(mets) + if subsystem is not None: + rxn.subsystem = subsystem + return rxn + + +def _met(mid, formula, charge=0): + m = cobra.Metabolite(mid, compartment="c") + m.formula, m.charge = formula, charge + return m + + +@pytest.mark.parametrize("subsystem", ["Pool reactions", "Artificial reactions", + ["Pool reactions"], ["Artificial reactions", "x"]]) +def test_lumped_subsystems_are_skipped(subsystem): + rxn = _rxn("MAR00001", {}, subsystem) + assert balanceTest._subsystems(rxn) & balanceTest.LUMPED_SUBSYSTEMS + + +@pytest.mark.parametrize("subsystem", ["Glycolysis", "", None, [], ["Glycolysis"]]) +def test_other_subsystems_are_not_skipped(subsystem): + rxn = _rxn("MAR00001", {}, subsystem) + assert not balanceTest._subsystems(rxn) & balanceTest.LUMPED_SUBSYSTEMS + + +def test_subsystems_accepts_a_string_or_a_list(): + assert balanceTest._subsystems(_rxn("R", {}, "Pool reactions")) == {"Pool reactions"} + assert balanceTest._subsystems(_rxn("R", {}, ["a", "b"])) == {"a", "b"} + assert balanceTest._subsystems(_rxn("R", {}, None)) == set() + + +def test_R_and_X_are_balanced_as_elements(): + """A reaction that balances in C and H but not in R is still an imbalance.""" + a, b = _met("a_c", "C2H4R"), _met("b_c", "C2H4") + rxn = _rxn("MAR00002", {a: -1, b: 1}, "Glycolysis") + cobra.Model("m").add_reactions([rxn]) + assert rxn.check_mass_balance().get("R") == -1 + + c, d = _met("c_c", "X"), _met("d_c", "X") + ok = _rxn("MAR00003", {c: -1, d: 1}, "Glycolysis") + cobra.Model("m2").add_reactions([ok]) + assert not ok.check_mass_balance() diff --git a/data/testResults/README.md b/data/testResults/README.md index 82a7b6934..d58180527 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -67,7 +67,9 @@ Metabolites with no chemical formula. They are silently skipped by the mass-bala Metabolites with no charge, for the same reason as the formula check. #### Mass-imbalanced reactions -Reactions whose elemental sums do not balance, from cobrapy's `check_mass_balance()`. Boundary reactions (exchange/demand/sink) and biomass are excluded, since they are not expected to balance. +Reactions whose elemental sums do not balance, from cobrapy's `check_mass_balance()`. Boundary reactions (exchange/demand/sink), biomass, and the lumped reactions of the `Pool reactions` and `Artificial reactions` subsystems are excluded, since they are not expected to balance: a pool reaction stands for many species at once and carries fractional coefficients against the `R` pseudo-element, and an artificial conversion lumps a whole class of metabolites into one pool. + +`R` and `X` are treated as elements of their own rather than ignored, so a reaction using them is still expected to balance in them. Several do not, and that is a finding rather than noise. #### Charge-imbalanced reactions Reactions whose charge sums do not balance, with the same exclusions as above. From e5e50ecbddd5312b783b979b458ca3de98969114 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Thu, 8 Oct 2026 23:20:21 +0200 Subject: [PATCH 02/44] fix: metFormula of the protein placeholders that cross two conventions (#1153) Human-GEM writes a protein-bound residue in two ways. The glycosylation, glycosaminoglycan and GPI networks use X for the whole protein, residue included, and spell out only the attached group: [protein]-L-serine is XH and Xyl-L-Ser-[protein] is C5H9O4X. The protein- and peptide-residue metabolites instead spell out the full residue plus the flanking carbonyl and amide NH, with R2 for the two chain continuations. Subtracting the free amino acid minus H2O from each of the fourteen [protein]/peptide/histone residue metabolites leaves CHNOR2 in eleven cases; the two aspartates differ only by the protonation state of the free acid, and peptidylglycine covers two residues. MAM00196 [protein] carried X while serving as the empty residue slot of ten R2-convention reactions, so each of them lost an X and gained an R2. Under the family convention an unoccupied slot is one peptide bond with two chain continuations, CHNOR2. Its only X-convention partner, MAM02339 L-arginyl-protein, moves with it to C7H14N5O2R2, the formula MAM00197 [protein]-L-arginine already carries for the same residue. This balances MAR06974, MAR06978, MAR07165, MAR07616, MAR07621, MAR07625, MAR08029 and MAR09735, four of which have GPRs, and takes the mass-imbalanced count from 27 to 19. Nothing becomes unbalanced: MAM02339 appears in MAR09541 alone, which stays balanced. MAR07197 and MAR07282 remain unbalanced. They convert [protein] into the X-convention [protein]-L-serine and [protein]-L-asparagine, whose XH formulas are required by fourteen balanced reactions of the glycosylation network, so their imbalance is restated rather than resolved. MAR13078 PROTEIN_BS is a biomass pseudo-reaction over fractional amino acid coefficients and cannot balance. Only metFormula changes. The stoichiometry, bounds, GPRs and metabolite charges are identical and growth stays at 138.5326986442, so gene essentiality cannot move. --- model/Human-GEM.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 9c5fdfee6..194ea2a00 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -2715,7 +2715,7 @@ - name: "[protein]" - compartment: c - charge: 0.0 - - formula: X + - formula: CHNOR2 - metFrom: HMRdatabase - !!omap - id: MAM00197c @@ -27447,7 +27447,7 @@ - name: L-arginyl-protein - compartment: c - charge: 1.0 - - formula: C6H13N4OX + - formula: C7H14N5O2R2 - metFrom: HMRdatabase - !!omap - id: MAM02340c @@ -56983,7 +56983,7 @@ - name: "[protein]" - compartment: r - charge: 0.0 - - formula: X + - formula: CHNOR2 - !!omap - id: MAM10012c - name: cofactor_pool_biomass From dd1eefd61d52b13f3f4a249ea4b51418221a91fb Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Fri, 9 Oct 2026 09:52:16 +0200 Subject: [PATCH 03/44] fix: metCharge of placeholder carriers that do not encode what they carry (#1153) A one-electron carrier pair must differ by one charge unit, as ferricytochrome C (+3) and ferrocytochrome C (+2) already do in this model. The three carrier pairs written as the X placeholder instead have both members at zero, so every reaction that reoxidises them is short by exactly the protons it consumes. Charging the reduced member keeps the oxidized form at its current value and matches the direction of the cytochrome C pair: MAM02827 reduced adrenal ferredoxin 0 -> -1 MAM02828 reduced ferredoxin 0 -> -1 (c and m) MAM01825 ferrocytochrome B5 0 -> -1 MAM00137, the ADP-D-ribosylated acceptor of MAR09487, spells out the two phosphates of the transferred ADP-ribosyl but carries charge zero. The same group takes MAM00197 [protein]-L-arginine from +1 to -1 in MAM00215, so it is worth -2 here as well. MAM01266 activated methyl group is the methyl that SAM donates in MAR04842, which turns the sulfonium SAM (+1) into neutral SAH. A methyl leaving a sulfonium is a methyl cation, so 0 -> +1. This balances MAR01932, MAR01934, MAR01935, MAR01942, MAR01950, MAR02126, MAR02128, MAR03992, MAR04842, MAR07741 and MAR09487, and takes the charge-imbalanced count from 160 to 149. Nothing becomes unbalanced. Only metCharge changes. Stoichiometry, bounds, GPRs, formulas and the reaction and metabolite sets are identical to develop and growth stays at 138.5326986442, so gene essentiality cannot move. --- model/Human-GEM.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 194ea2a00..bb993c657 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -2133,7 +2133,7 @@ - id: MAM00137c - name: (ADP-D-ribosyl)n-acceptor - compartment: c - - charge: 0.0 + - charge: -2.0 - formula: C15H19N5O13P2X - metFrom: HMRdatabase - !!omap @@ -13772,7 +13772,7 @@ - id: MAM01266c - name: activated methyl group - compartment: c - - charge: 0.0 + - charge: 1.0 - formula: CH3 - metFrom: HMRdatabase - !!omap @@ -21553,7 +21553,7 @@ - id: MAM01825c - name: ferrocytochrome B5 - compartment: c - - charge: 0.0 + - charge: -1.0 - formula: X - metFrom: HMRdatabase - !!omap @@ -33821,21 +33821,21 @@ - id: MAM02827c - name: reduced adrenal ferredoxin - compartment: c - - charge: 0.0 + - charge: -1.0 - formula: X - metFrom: HMRdatabase - !!omap - id: MAM02828c - name: reduced ferredoxin - compartment: c - - charge: 0.0 + - charge: -1.0 - formula: X - metFrom: HMRdatabase - !!omap - id: MAM02828m - name: reduced ferredoxin - compartment: m - - charge: 0.0 + - charge: -1.0 - formula: X - metFrom: HMRdatabase - !!omap From 1bb5a74b2dd255463e8aa5d34b544853f59f4e97 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Fri, 9 Oct 2026 09:58:43 +0200 Subject: [PATCH 04/44] fix: give lepidimoide its formula and charge instead of the X placeholder (#1153) MAM02357 lepidimoide is a defined disaccharide carrying the placeholder formula X, which is why the "metabolites missing formula" check passes it: X counts as a formula. Its stored InChI ends in /q;+1/p-1 over C12H18O10.Na, that is, the sodium salt of an anion that has lost one proton, and RDKit reads the stored SMILES as C12H17NaO10 at charge 0 in the committed qc_structure_consistency.csv. Both give the same entity for the model to carry: C12H17O10 at -1. It appears only in MAR01852 and MAR01859, on both sides of each, so no balance changes. Its two structure-consistency rows stay for now: metSmiles and metInChI both still carry the sodium counter-ion, and they should be dropped together, with RDKit on hand to verify the result, as part of the metSmiles batch rather than by hand here. --- model/Human-GEM.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index bb993c657..358ecc7e0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -27691,15 +27691,15 @@ - id: MAM02357c - name: lepidimoide - compartment: c - - charge: 0.0 - - formula: X + - charge: -1.0 + - formula: C12H17O10 - metFrom: HMRdatabase - !!omap - id: MAM02357e - name: lepidimoide - compartment: e - - charge: 0.0 - - formula: X + - charge: -1.0 + - formula: C12H17O10 - metFrom: HMRdatabase - !!omap - id: MAM02358m From cfe909ece9ea26060fefcbe13ae01d3e966a4297 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Fri, 9 Oct 2026 12:52:18 +0200 Subject: [PATCH 05/44] fix: identify the lumped pseudo-reactions, not just their subsystems (#1153) An elemental balance is not defined for a reaction whose coefficients average over a class of species. Protein assembly and protein degradation consist of such reactions throughout, alongside the pool and artificial subsystems. The fifteen filed under an ordinary subsystem are excluded by identifier, each with what it lumps, and the list is audited on every run so an entry the model no longer needs is reported. --- code/test/balanceTest.py | 115 ++++++++++++++++++++++------ code/test/unit/test_balance_test.py | 29 +++++++ data/testResults/README.md | 4 +- 3 files changed, 122 insertions(+), 26 deletions(-) diff --git a/code/test/balanceTest.py b/code/test/balanceTest.py index 318dea905..433feeade 100644 --- a/code/test/balanceTest.py +++ b/code/test/balanceTest.py @@ -3,16 +3,20 @@ Uses cobrapy's Reaction.check_mass_balance(), which reports both elemental (mass) and charge imbalances in a single call. Boundary reactions -(exchange/demand/sink), the biomass reaction and the lumped reactions of the -"Pool reactions" and "Artificial reactions" subsystems are excluded, since they -are not expected to balance: a pool reaction stands for many species at once -and carries fractional coefficients against the R pseudo-element, and an -artificial conversion lumps a whole class of metabolites into one pool. +(exchange/demand/sink), the biomass reaction and the lumped pseudo-reactions +are excluded, since an elemental balance is not defined for them: a lumped +pseudo-reaction stands for a whole class of species at once, so its +coefficients are an average over that class rather than a stoichiometry. + +Lumping is recognised two ways. Four subsystems consist of lumped reactions +throughout (LUMPED_SUBSYSTEMS). The lumped reactions filed elsewhere are listed +by identifier, with what each one lumps (LUMPED_REACTIONS); that list is +audited on every run, so an entry that the model no longer needs is reported +rather than left to rot. R and X are left as elements of their own, not ignored. A reaction that uses -them is still expected to balance in them, and several do not: the -"[protein] to [protein]-L-" reactions are off by one X and two R, -which is a finding rather than noise (#1153). +them is still expected to balance in them, and several do not, which is a +finding rather than noise (#1153). The unbalanced reactions are written, sorted, to data/testResults/balance_results.csv, so that a pull request introducing a new @@ -25,9 +29,38 @@ import cobra -# A reaction in one of these subsystems lumps many species into a single -# pseudo-reaction, so an elemental balance is not defined for it. -LUMPED_SUBSYSTEMS = frozenset({"Pool reactions", "Artificial reactions"}) +# Every reaction in one of these subsystems lumps many species into a single +# pseudo-reaction: a pool stands for the mixture of its members, an artificial +# conversion for a whole class of metabolites, and protein assembly and +# degradation for the translation and proteolysis of a named protein, counted +# per amino-acid residue. +LUMPED_SUBSYSTEMS = frozenset({ + "Pool reactions", + "Artificial reactions", + "Protein assembly", + "Protein degradation", +}) + +# The lumped pseudo-reactions filed under an ordinary subsystem, and what each +# one lumps. A reaction belongs here only when its coefficients average over a +# class of species, so that no single elemental balance exists for it; a +# reaction that is merely unbalanced does not. +LUMPED_REACTIONS = { + # A pool metabolite whose formula spells out only what its members have in + # common, resolved into a weighted mixture of those members. + "MAR00015": "NEFA blood pool in to its member fatty acids", + "MAR00016": "member fatty acids to NEFA blood pool out", + "MAR00017": "SMCFA blood pool to its member fatty acids", + "MAR03537": "cholesterol-ester plasma pool to its member esters", + "MAR03622": "cholesterol-ester plasma pool to its member esters", + # DNA and RNA carry the formula of one average nucleotide, polymerised from + # and hydrolysed to a weighted mixture of the four (deoxy)nucleotides. + "MAR07160": "DNA from a mixture of dNTPs", + "MAR07161": "RNA from a mixture of NTPs", + "MAR07162": "RNA to a mixture of NDPs", + "MAR07163": "DNA to a mixture of dNMPs", + "MAR07164": "RNA to a mixture of NMPs", +} def _subsystems(rxn): @@ -38,35 +71,62 @@ def _subsystems(rxn): return {str(sub)} if sub else set() +def _is_lumped(rxn): + """Whether the reaction stands for a whole class of species at once.""" + return rxn.id in LUMPED_REACTIONS or bool(_subsystems(rxn) & LUMPED_SUBSYSTEMS) + + +def _stale_lumped_entries(model, unbalanced_ids): + """Entries of LUMPED_REACTIONS the model no longer needs. + + An identifier that is gone from the model, or whose reaction now balances + in both mass and charge, no longer excludes anything and should be dropped + from the list. + """ + stale = [] + for rid in sorted(LUMPED_REACTIONS): + if rid not in model.reactions: + stale.append(f"{rid} (not in the model)") + elif rid not in unbalanced_ids: + stale.append(f"{rid} (balances)") + return stale + + def main(): model = cobra.io.load_yaml_model("model/Human-GEM.yml") rows = [] errored = [] + unbalanced_ids = set() + n_lumped = 0 for rxn in model.reactions: if rxn.boundary: continue if "biomass" in rxn.id.lower() or "biomass" in (rxn.name or "").lower(): continue - if _subsystems(rxn) & LUMPED_SUBSYSTEMS: - continue try: imbalance = rxn.check_mass_balance() except Exception as exc: # noqa: BLE001 - record, do not silently drop # A reaction whose balance cannot be evaluated (usually a malformed # formula) is a finding, not something to hide: record it as its own # row so it shows up in the committed diff and the count. - errored.append(rxn.id) - rows.append((rxn.id, rxn.name or "", f"check_failed:{exc}", "")) + if not _is_lumped(rxn): + errored.append(rxn.id) + rows.append((rxn.id, rxn.name or "", f"check_failed:{exc}", "")) + continue + if not imbalance: + continue + unbalanced_ids.add(rxn.id) + if _is_lumped(rxn): + n_lumped += 1 continue - if imbalance: - mass = {k: v for k, v in imbalance.items() if k != "charge"} - charge = imbalance.get("charge", 0) - rows.append(( - rxn.id, - rxn.name or "", - ";".join(f"{k}:{v:g}" for k, v in sorted(mass.items())), - f"{charge:g}" if charge else "", - )) + mass = {k: v for k, v in imbalance.items() if k != "charge"} + charge = imbalance.get("charge", 0) + rows.append(( + rxn.id, + rxn.name or "", + ";".join(f"{k}:{v:g}" for k, v in sorted(mass.items())), + f"{charge:g}" if charge else "", + )) rows.sort() with open("data/testResults/balance_results.csv", "w", newline="") as fh: writer = csv.writer(fh) @@ -76,11 +136,16 @@ def main(): n_charge = sum(1 for r in rows if r[3]) print( f"Unbalanced reactions (excluding boundary, biomass and lumped): {len(rows)} " - f"({n_mass} mass, {n_charge} charge, {len(errored)} could not be checked)" + f"({n_mass} mass, {n_charge} charge, {len(errored)} could not be checked); " + f"{n_lumped} lumped pseudo-reaction(s) excluded" ) if errored: print(f"::warning::{len(errored)} reaction(s) could not be balance-checked: " f"{';'.join(errored[:20])}{' ...' if len(errored) > 20 else ''}") + stale = _stale_lumped_entries(model, unbalanced_ids) + if stale: + print(f"::warning::{len(stale)} entr(y/ies) of LUMPED_REACTIONS are no longer " + f"needed and can be dropped from code/test/balanceTest.py: {'; '.join(stale)}") if __name__ == "__main__": diff --git a/code/test/unit/test_balance_test.py b/code/test/unit/test_balance_test.py index 4616f6865..b643f0d46 100644 --- a/code/test/unit/test_balance_test.py +++ b/code/test/unit/test_balance_test.py @@ -50,3 +50,32 @@ def test_R_and_X_are_balanced_as_elements(): ok = _rxn("MAR00003", {c: -1, d: 1}, "Glycolysis") cobra.Model("m2").add_reactions([ok]) assert not ok.check_mass_balance() + + +@pytest.mark.parametrize("subsystem", ["Protein assembly", "Protein degradation"]) +def test_protein_assembly_and_degradation_are_lumped(subsystem): + assert balanceTest._is_lumped(_rxn("MAR05151", {}, subsystem)) + + +def test_listed_reactions_are_lumped_whatever_their_subsystem(): + for rid in balanceTest.LUMPED_REACTIONS: + assert balanceTest._is_lumped(_rxn(rid, {}, "Nucleotide metabolism")) + + +def test_an_unlisted_reaction_in_an_ordinary_subsystem_is_not_lumped(): + assert not balanceTest._is_lumped(_rxn("MAR09999", {}, "Nucleotide metabolism")) + + +def test_every_listed_reason_says_what_is_lumped(): + assert all(len(reason) > 10 for reason in balanceTest.LUMPED_REACTIONS.values()) + + +def test_stale_entries_report_missing_and_balanced_reactions(): + model = cobra.Model("m") + kept, dropped = sorted(balanceTest.LUMPED_REACTIONS)[:2] + model.add_reactions([_rxn(kept, {}), _rxn(dropped, {})]) + stale = balanceTest._stale_lumped_entries(model, {kept}) + assert f"{dropped} (balances)" in stale + assert not any(line.startswith(kept) for line in stale) + assert sum(1 for line in stale if "(not in the model)" in line) == \ + len(balanceTest.LUMPED_REACTIONS) - 2 diff --git a/data/testResults/README.md b/data/testResults/README.md index d58180527..e504cc937 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -67,7 +67,9 @@ Metabolites with no chemical formula. They are silently skipped by the mass-bala Metabolites with no charge, for the same reason as the formula check. #### Mass-imbalanced reactions -Reactions whose elemental sums do not balance, from cobrapy's `check_mass_balance()`. Boundary reactions (exchange/demand/sink), biomass, and the lumped reactions of the `Pool reactions` and `Artificial reactions` subsystems are excluded, since they are not expected to balance: a pool reaction stands for many species at once and carries fractional coefficients against the `R` pseudo-element, and an artificial conversion lumps a whole class of metabolites into one pool. +Reactions whose elemental sums do not balance, from cobrapy's `check_mass_balance()`. Boundary reactions (exchange/demand/sink), biomass and the lumped pseudo-reactions are excluded, since an elemental balance is not defined for them: a lumped pseudo-reaction stands for a whole class of species at once, so its coefficients are an average over that class rather than a stoichiometry. + +`balanceTest.py` recognises lumping two ways. Four subsystems consist of lumped reactions throughout, and are excluded wholesale (`LUMPED_SUBSYSTEMS`): `Pool reactions`, where a pool stands for the mixture of its members; `Artificial reactions`, where a conversion lumps a whole class of metabolites; and `Protein assembly` and `Protein degradation`, which translate and hydrolyse a named protein counted per amino-acid residue. The lumped reactions filed under an ordinary subsystem are listed by identifier instead, each with what it lumps (`LUMPED_REACTIONS`): five reactions that resolve a fatty-acid or cholesterol-ester pool into a weighted mixture of its members, and the five that polymerise and hydrolyse `DNA` and `RNA`, whose formulas are those of one average nucleotide. Every run audits that list and warns about an entry the model no longer needs, so it cannot quietly go stale. Subsystems are left as curated; the identifiers keep the exclusion in the test rather than relabelling reactions that users expect to find in their pathway. `R` and `X` are treated as elements of their own rather than ignored, so a reaction using them is still expected to balance in them. Several do not, and that is a finding rather than noise. From 732099470c313f20644c306d4500585dc6f9ba35 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Fri, 9 Oct 2026 12:58:40 +0200 Subject: [PATCH 06/44] fix: name the poly(ADP-ribose) acceptors after the chain they carry (#1153) MAR09487 transfers an ADP-ribosyl group from NAD+ onto the acceptor and releases nicotinamide, and its stoichiometry puts that group on MAM00137. The two names stated the opposite, so the equation read as a chain losing a unit while gaining one in mass. --- model/Human-GEM.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 358ecc7e0..6fd9a6d22 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -2124,14 +2124,14 @@ - metFrom: HMRdatabase - !!omap - id: MAM00136c - - name: (ADP-D-ribosyl)n+1-acceptor + - name: (ADP-D-ribosyl)n-acceptor - compartment: c - charge: 0.0 - formula: X - metFrom: HMRdatabase - !!omap - id: MAM00137c - - name: (ADP-D-ribosyl)n-acceptor + - name: (ADP-D-ribosyl)n+1-acceptor - compartment: c - charge: -2.0 - formula: C15H19N5O13P2X From 19a3aec388e8c6cc42b16c599dd97b2fc10c4a2d Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 01:29:25 +0100 Subject: [PATCH 07/44] feat: applyCurationTable changes gene rules, equations and references The table fields now include gene_reaction_rule (written with gene symbols), metabolites, references and name of reactions, and a gene row deletes a gene that no reaction uses. #1153 --- code/modelCuration/README.md | 2 +- code/modelCuration/applyCurationTable.py | 91 +++++++++++++++++++-- code/test/unit/test_apply_curation_table.py | 59 +++++++++++++ 3 files changed, 142 insertions(+), 10 deletions(-) diff --git a/code/modelCuration/README.md b/code/modelCuration/README.md index 78666d3ae..6e5509e9c 100644 --- a/code/modelCuration/README.md +++ b/code/modelCuration/README.md @@ -8,4 +8,4 @@ The one-off curation scripts from the Human1 series (2018-2024) have been remove Each script edits the model files in place and takes `--dry-run`. The per-entity table of a scripted change is in `data/modelCuration/`, and the commit that made the change gives the command. - `backfillDeprecatedColumns.py --table data/modelCuration/.tsv` gives `data/deprecatedIdentifiers/deprecatedReactions.tsv` and `deprecatedMetabolites.tsv` the columns of `model/reactions.tsv` and `model/metabolites.tsv` that they lack, and fills cells from a table (list, id, column, value). `--dry-run` reports what would change. -- `applyCurationTable.py --table data/modelCuration/.tsv` applies a per-entity table of annotation changes (entity, field, before, after) to `model/Human-GEM.yml` (reaction, metabolite and gene names, metabolite formula and charge, reaction EC numbers and rxnFrom) and to the columns of `model/reactions.tsv`, `model/metabolites.tsv` and `model/genes.tsv`. A row is applied when the current value equals `before`; any other value stops the script before it writes. The files are edited line by line, so the lines the table does not change stay as they are. `--dry-run` reports what would change. +- `applyCurationTable.py --table data/modelCuration/.tsv` applies a per-entity table of annotation changes (entity, field, before, after) to `model/Human-GEM.yml` (reaction, metabolite and gene names, metabolite formula and charge, reaction EC numbers, rxnFrom, references, gene rules written with gene symbols, and equations written as `id:coefficient` pairs; a gene row with before `present` and an empty after deletes a gene that no reaction uses) and to the columns of `model/reactions.tsv`, `model/metabolites.tsv` and `model/genes.tsv`. A row is applied when the current value equals `before`; any other value stops the script before it writes. The files are edited line by line, so the lines the table does not change stay as they are. `--dry-run` reports what would change. diff --git a/code/modelCuration/applyCurationTable.py b/code/modelCuration/applyCurationTable.py index 6d2b2785c..a04ecf6a7 100644 --- a/code/modelCuration/applyCurationTable.py +++ b/code/modelCuration/applyCurationTable.py @@ -6,11 +6,16 @@ changed value; further columns (a note, a source) are ignored. entity is a reaction (MAR), metabolite (MAM) or gene (ENSG) id, and field is one of: - - name (reactions, metabolites and genes), formula and charge (metabolites), ec-code and - rxnFrom (reactions), in model/Human-GEM.yml; several EC numbers are joined by ";"; + - name (reactions, metabolites and genes), formula and charge (metabolites), ec-code, + rxnFrom, references and gene_reaction_rule (reactions) and metabolites (reactions), in + model/Human-GEM.yml; several EC numbers are joined by ";"; gene_reaction_rule is written + with gene symbols, which the script maps to the Ensembl ids of the genes section; + metabolites is a ";"-separated list of id:coefficient pairs; - a column of model/reactions.tsv, model/metabolites.tsv or model/genes.tsv. -An empty value stands for an absent field or an empty cell. A row is applied when the +An empty value stands for an absent field or an empty cell. A gene row (field gene, before +present, after empty) deletes the gene from the genes section of the YAML and from +model/genes.tsv; it is refused while a reaction still uses the gene. A row is applied when the current value equals before. A value that already equals after is left as it is; any other value is reported and nothing is written. The files are edited in place, line by line, so every line that the table does not change stays byte-identical. --dry-run reports what @@ -31,7 +36,8 @@ TSV = {"MAR": Path("model/reactions.tsv"), "MAM": Path("model/metabolites.tsv"), "ENSG": Path("model/genes.tsv")} SECTION = {"MAR": "reactions", "MAM": "metabolites", "ENSG": "genes"} -YAML_FIELDS = {"MAR": {"name", "ec-code", "rxnFrom"}, "MAM": {"name", "formula", "charge"}, +YAML_FIELDS = {"MAR": {"name", "ec-code", "rxnFrom", "references", "gene_reaction_rule", "metabolites"}, + "MAM": {"name", "formula", "charge"}, "ENSG": {"name"}} # Field order of a reaction entry, as raven_toolbox.io.write_yaml_model writes it. REACTION_ORDER = ["id", "name", "metabolites", "lower_bound", "upper_bound", "gene_reaction_rule", @@ -157,6 +163,10 @@ def get(self, section: str, entry: str, field: str) -> str: return ";".join(codes) if field not in blocks: return "" + if field == "metabolites": + first, end = blocks[field] + pairs = (self.lines[i][len(" - "):].split(": ") for i in range(first + 1, end)) + return ";".join(f"{met}:{float(coefficient)!r}" for met, coefficient in pairs) line = self.lines[blocks[field][0]] return parse(line.split(": ", 1)[1]) if ": " in line else "" @@ -165,6 +175,10 @@ def set(self, section: str, entry: str, field: str, value: str) -> None: blocks = self.fields(section, entry) if field == "ec-code": self._set_ec(blocks, entry, value) + elif field == "metabolites": + first, end = blocks[field] + pairs = [pair.rsplit(":", 1) for pair in value.split(";")] + self.lines[first + 1:end] = [f" - {met}: {float(coefficient)!r}" for met, coefficient in pairs] else: text = charge_text(value) if field == "charge" else render(value) if field in blocks: @@ -176,8 +190,11 @@ def set(self, section: str, entry: str, field: str, value: str) -> None: self.lines[first] = f" - {field}: {text}" elif value != "": self.lines.insert(self._position(blocks, entry, field), f" - {field}: {text}") - if len(self.lines) != n_lines: - self.index() + delta = len(self.lines) - n_lines + if delta: + start, end = self.entries[(section, entry)] + self.entries = {key: (a + delta, b + delta) if a >= end else (a, b + delta) if key == (section, entry) else (a, b) + for key, (a, b) in self.entries.items()} def _set_ec(self, blocks: dict, entry: str, value: str) -> None: codes = [c for c in value.split(";") if c] @@ -206,6 +223,23 @@ def _position(self, blocks: dict, entry: str, field: str) -> int: return min(starts) return max(end for _, end in blocks.values()) + def delete_entry(self, section: str, entry: str) -> None: + start, end = self.entries[(section, entry)] + del self.lines[start:end] + self.index() + + def rule_users(self, gene: str) -> list[str]: + """The reactions whose gene_reaction_rule contains the gene id.""" + users = [] + for (section, entry) in self.entries: + if section == "reactions" and gene in self.get(section, entry, "gene_reaction_rule").split(): + users.append(entry) + return users + + def gene_ids(self) -> dict: + """Gene symbol -> Ensembl id of the genes section.""" + return {self.get("genes", g, "name"): g for (section, g) in self.entries if section == "genes"} + def save(self) -> None: self.path.write_text("\n".join(self.lines), encoding="utf-8") @@ -231,6 +265,10 @@ def set(self, key: str, column: str, value: str) -> None: values[self.header.index(column)] = value self.lines[self.rows[key]] = "\t".join(values) + def delete(self, key: str) -> None: + del self.lines[self.rows[key]] + self.rows = {line.split("\t", 1)[0]: i for i, line in enumerate(self.lines[1:], 1) if line} + def save(self) -> None: self.path.write_text("\n".join(self.lines), encoding="utf-8") @@ -243,6 +281,19 @@ def kind_of(entity: str) -> str: raise ValueError(f"{entity}: not a reaction, metabolite or gene id") +def rule_to_ids(rule: str, genes: dict) -> str: + """A gene_reaction_rule written with gene symbols, with the Ensembl ids of the genes.""" + out = [] + for token in re.findall(r"\(|\)|[^\s()]+", rule): + if token in ("(", ")", "and", "or"): + out.append(token) + elif token in genes: + out.append(genes[token]) + else: + raise ValueError(f"{token}: not a gene symbol of the genes section") + return " ".join(out).replace("( ", "(").replace(" )", ")") + + def read_table(path: Path) -> list[dict]: with path.open(newline="", encoding="utf-8") as handle: rows = list(csv.DictReader(handle, delimiter="\t", quoting=csv.QUOTE_NONE)) @@ -258,11 +309,33 @@ def apply(rows: list[dict], root: Path = Path(".")) -> tuple[Counter, list[str], model = Model(root / YML) tables = {k: Table(root / p) for k, p in TSV.items()} changed, problems = Counter(), [] + symbols = model.gene_ids() if any(r["field"] == "gene_reaction_rule" for r in rows) else {} for row in rows: entity, field = row["entity"], row["field"] before, after = row["before"], row["after"] kind = kind_of(entity) - if field in YAML_FIELDS[kind]: + if kind == "ENSG" and field == "gene": + if (SECTION[kind], entity) not in model.entries: + if entity not in tables[kind].rows: + continue + problems.append(f"{entity}: in {TSV[kind]} but not in {YML}") + continue + if before != "present" or after != "": + problems.append(f"{entity} gene: only present -> empty is supported") + continue + users = model.rule_users(entity) + if users: + problems.append(f"{entity} gene: still in the rule of {', '.join(users[:5])}") + continue + model.delete_entry(SECTION[kind], entity) + tables[kind].delete(entity) + elif field in YAML_FIELDS[kind]: + if field == "gene_reaction_rule": + after = rule_to_ids(after, symbols) + try: + before = rule_to_ids(before, symbols) + except ValueError: + before = None # a gene of the old rule has been deleted since section = SECTION[kind] if (section, entity) not in model.entries: problems.append(f"{entity}: not in {YML}") @@ -271,8 +344,8 @@ def apply(rows: list[dict], root: Path = Path(".")) -> tuple[Counter, list[str], same = same_charge if field == "charge" else str.__eq__ if same(current, after): continue - if not same(current, before): - problems.append(f"{entity} {field}: {current!r}, expected {before!r}") + if before is None or not same(current, before): + problems.append(f"{entity} {field}: {current!r}, expected {row['before']!r}") continue model.set(section, entity, field, after) else: diff --git a/code/test/unit/test_apply_curation_table.py b/code/test/unit/test_apply_curation_table.py index 8c9b508d1..f0584d2ff 100644 --- a/code/test/unit/test_apply_curation_table.py +++ b/code/test/unit/test_apply_curation_table.py @@ -131,3 +131,62 @@ def test_a_value_that_differs_from_before_is_reported(root): def test_a_value_already_set_is_skipped(root): changed, problems = run(root, [("MAR00002", "rxnMetaNetXID", "MNXR9", "MNXR2")]) assert problems == [] and not changed + + +def test_gene_reaction_rule_written_with_symbols(root): + changed, problems = run(root, [("MAR00002", "gene_reaction_rule", "GLYK", "GLYK or GLYK")]) + assert problems == [] and changed["gene_reaction_rule"] == 1 + assert " - gene_reaction_rule: ENSG00000000001 or ENSG00000000001\n" in yml(root) + + +def test_gene_reaction_rule_removed(root): + run(root, [("MAR00002", "gene_reaction_rule", "GLYK", "")]) + assert "gene_reaction_rule" not in yml(root) + + +def test_gene_reaction_rule_with_unknown_symbol_is_an_error(root): + with pytest.raises(ValueError): + run(root, [("MAR00002", "gene_reaction_rule", "GLYK", "NOPE")]) + + +def test_metabolites_replaced_in_the_given_order(root): + changed, problems = run(root, [("MAR00001", "metabolites", "MAM00001c:-1.0", "MAM00001c:-1.0;MAM00001c:2.0")]) + assert problems == [] and changed["metabolites"] == 1 + assert " - metabolites: !!omap\n - MAM00001c: -1.0\n - MAM00001c: 2.0\n - lower_bound" in yml(root) + + +def test_references_added_before_rxnfrom(root): + run(root, [("MAR00002", "references", "", "doi:10.1/x")]) + assert " - references: doi:10.1/x\n - rxnFrom: HMRdatabase" in yml(root) + + +def test_unused_gene_is_deleted_from_both_files(root): + changed, problems = run(root, [("MAR00002", "gene_reaction_rule", "GLYK", ""), + ("ENSG00000000001", "gene", "present", "")]) + assert problems == [] and changed["gene"] == 1 + assert "ENSG00000000001" not in yml(root) + assert "ENSG00000000001" not in (root / "model" / "genes.tsv").read_text(encoding="utf-8") + + +def test_gene_still_in_a_rule_is_kept(root): + changed, problems = run(root, [("ENSG00000000001", "gene", "present", "")]) + assert problems == ["ENSG00000000001 gene: still in the rule of MAR00002"] + assert "ENSG00000000001" in yml(root) + + +def test_edits_that_change_the_line_count_leave_later_entries_findable(root): + changed, problems = run(root, [ + ("MAR00001", "references", "PMID:1", ""), + ("MAR00001", "gene_reaction_rule", "", "GLYK"), + ("MAR00002", "references", "", "doi:10.1/x"), + ("MAR00002", "name", "glycine kinase", "glycerate kinase")]) + assert problems == [] and sum(changed.values()) == 4 + text = yml(root) + assert " - references: PMID:1" not in text + assert " - name: glycerate kinase" in text and " - references: doi:10.1/x\n - rxnFrom" in text + + +def test_rule_row_is_skipped_when_a_gene_of_the_old_rule_was_deleted(root): + run(root, [("MAR00002", "gene_reaction_rule", "GLYK", ""), ("ENSG00000000001", "gene", "present", "")]) + changed, problems = run(root, [("MAR00002", "gene_reaction_rule", "GLYK or GONE", "")]) + assert problems == [] and not changed From fbced311ec8bf3e5e29833fcb4993dfb3b3bd5b3 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 10:43:16 +0100 Subject: [PATCH 08/44] fix: aflatoxin B1 dialdehyde reductions take NADPH AKR7A2 and AKR7A3 reduce the dialdehyde to the monoalcohols and the dialcohol with NADPH. The reactions wrote the two electrons as protons, which left each of them short by two charges. Generated by `code/modelCuration/applyCurationTable.py --table data/modelCuration/aflatoxinDialdehydeReductions.tsv`. #1153 --- .../aflatoxinDialdehydeReductions.tsv | 9 +++++++++ model/Human-GEM.yml | 20 +++++++++++++++---- 2 files changed, 25 insertions(+), 4 deletions(-) create mode 100644 data/modelCuration/aflatoxinDialdehydeReductions.tsv diff --git a/data/modelCuration/aflatoxinDialdehydeReductions.tsv b/data/modelCuration/aflatoxinDialdehydeReductions.tsv new file mode 100644 index 000000000..c8d75d94d --- /dev/null +++ b/data/modelCuration/aflatoxinDialdehydeReductions.tsv @@ -0,0 +1,9 @@ +entity field before after +MAR07025 metabolites MAM00229c:1.0;MAM01294c:-1.0;MAM02039c:-2.0 MAM00229c:1.0;MAM01294c:-1.0;MAM02039c:-1.0;MAM02554c:1.0;MAM02555c:-1.0 +MAR07025 references doi:10.1021/tx010005p;doi:10.1093/carcin/20.7.1215 +MAR07027 metabolites MAM01294c:-1.0;MAM01318c:1.0;MAM02039c:-2.0 MAM01294c:-1.0;MAM01318c:1.0;MAM02039c:-1.0;MAM02554c:1.0;MAM02555c:-1.0 +MAR07027 references doi:10.1021/tx010005p;doi:10.1093/carcin/20.7.1215 +MAR07026 metabolites MAM00229c:-1.0;MAM01156c:1.0;MAM02039c:-3.0 MAM00229c:-1.0;MAM01156c:1.0;MAM02039c:-2.0;MAM02554c:1.0;MAM02555c:-1.0 +MAR07026 references doi:10.1021/tx010005p;doi:10.1093/carcin/20.7.1215 +MAR07028 metabolites MAM01156c:1.0;MAM01318c:-1.0;MAM02039c:-3.0 MAM01156c:1.0;MAM01318c:-1.0;MAM02039c:-2.0;MAM02554c:1.0;MAM02555c:-1.0 +MAR07028 references doi:10.1021/tx010005p;doi:10.1093/carcin/20.7.1215 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 6fd9a6d22..c16f27dc8 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -149148,7 +149148,9 @@ - metabolites: !!omap - MAM00229c: 1.0 - MAM01294c: -1.0 - - MAM02039c: -2.0 + - MAM02039c: -1.0 + - MAM02554c: 1.0 + - MAM02555c: -1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000053371 or ENSG00000162482 @@ -149157,6 +149159,7 @@ - annotation: !!omap - ec-code: - 1.1.1.- + - references: doi:10.1021/tx010005p;doi:10.1093/carcin/20.7.1215 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap @@ -149165,7 +149168,9 @@ - metabolites: !!omap - MAM00229c: -1.0 - MAM01156c: 1.0 - - MAM02039c: -3.0 + - MAM02039c: -2.0 + - MAM02554c: 1.0 + - MAM02555c: -1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000053371 or ENSG00000162482 @@ -149174,6 +149179,7 @@ - annotation: !!omap - ec-code: - 1.1.1.- + - references: doi:10.1021/tx010005p;doi:10.1093/carcin/20.7.1215 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap @@ -149182,7 +149188,9 @@ - metabolites: !!omap - MAM01294c: -1.0 - MAM01318c: 1.0 - - MAM02039c: -2.0 + - MAM02039c: -1.0 + - MAM02554c: 1.0 + - MAM02555c: -1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000053371 or ENSG00000162482 @@ -149191,6 +149199,7 @@ - annotation: !!omap - ec-code: - 1.1.1.- + - references: doi:10.1021/tx010005p;doi:10.1093/carcin/20.7.1215 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap @@ -149199,7 +149208,9 @@ - metabolites: !!omap - MAM01156c: 1.0 - MAM01318c: -1.0 - - MAM02039c: -3.0 + - MAM02039c: -2.0 + - MAM02554c: 1.0 + - MAM02555c: -1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000053371 or ENSG00000162482 @@ -149208,6 +149219,7 @@ - annotation: !!omap - ec-code: - 1.1.1.- + - references: doi:10.1021/tx010005p;doi:10.1093/carcin/20.7.1215 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap From 9457e0c3ce400eb4ec7c46a3283a068768f7f528 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 10:43:20 +0100 Subject: [PATCH 09/44] fix: formula of the dibenzo[a,l]pyrene diol epoxide and the proton of its formation The diol is a dihydrodiol (C24H16O2), so its epoxide is C24H16O3, not C24H14O3, and the monooxygenase consumes the proton instead of releasing it. Generated by `code/modelCuration/applyCurationTable.py --table data/modelCuration/dibenzoPyreneDiolEpoxide.tsv`. #1153 --- data/modelCuration/dibenzoPyreneDiolEpoxide.tsv | 5 +++++ model/Human-GEM.yml | 8 ++++---- 2 files changed, 9 insertions(+), 4 deletions(-) create mode 100644 data/modelCuration/dibenzoPyreneDiolEpoxide.tsv diff --git a/data/modelCuration/dibenzoPyreneDiolEpoxide.tsv b/data/modelCuration/dibenzoPyreneDiolEpoxide.tsv new file mode 100644 index 000000000..54c1c20fe --- /dev/null +++ b/data/modelCuration/dibenzoPyreneDiolEpoxide.tsv @@ -0,0 +1,5 @@ +entity field before after +MAM03385c formula C24H14O3 C24H16O3 +MAM03385r formula C24H14O3 C24H16O3 +MAR04088 metabolites MAM02039c:1.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0;MAM03384c:-1.0;MAM03385c:1.0 MAM02039c:-1.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0;MAM03384c:-1.0;MAM03385c:1.0 +MAR04090 metabolites MAM02039r:1.0;MAM02040r:1.0;MAM02554r:1.0;MAM02555r:-1.0;MAM02630r:-1.0;MAM03384r:-1.0;MAM03385r:1.0 MAM02039r:-1.0;MAM02040r:1.0;MAM02554r:1.0;MAM02555r:-1.0;MAM02630r:-1.0;MAM03384r:-1.0;MAM03385r:1.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index c16f27dc8..59af48275 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -42767,14 +42767,14 @@ - name: Dibenzo[A,L]Pyrene-11,12-Diol-13,14-Epoxide - compartment: c - charge: 0.0 - - formula: C24H14O3 + - formula: C24H16O3 - metFrom: Recon3D - !!omap - id: MAM03385r - name: Dibenzo[A,L]Pyrene-11,12-Diol-13,14-Epoxide - compartment: r - charge: 0.0 - - formula: C24H14O3 + - formula: C24H16O3 - metFrom: Recon3D - !!omap - id: MAM02999c @@ -212041,7 +212041,7 @@ - id: MAR04088 - name: Unspecific Monooxygenase - metabolites: !!omap - - MAM02039c: 1.0 + - MAM02039c: -1.0 - MAM02040c: 1.0 - MAM02554c: 1.0 - MAM02555c: -1.0 @@ -212061,7 +212061,7 @@ - id: MAR04090 - name: Unspecific Monooxygenase - metabolites: !!omap - - MAM02039r: 1.0 + - MAM02039r: -1.0 - MAM02040r: 1.0 - MAM02554r: 1.0 - MAM02555r: -1.0 From 45a8ea8e53abd46c1af46ef583500df5d7716254 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 10:43:25 +0100 Subject: [PATCH 10/44] fix: stoichiometry of the arginine nitric oxide synthase reaction The reaction is 2 L-arginine + 3 NADPH + 4 O2 + H+ => 2 L-citrulline + 2 NO + 3 NADP+ + 4 H2O (RHEA:19897). Generated by `code/modelCuration/applyCurationTable.py --table data/modelCuration/nitricOxideSynthaseStoichiometry.tsv`. #1153 --- .../nitricOxideSynthaseStoichiometry.tsv | 2 ++ model/Human-GEM.yml | 15 ++++++++------- 2 files changed, 10 insertions(+), 7 deletions(-) create mode 100644 data/modelCuration/nitricOxideSynthaseStoichiometry.tsv diff --git a/data/modelCuration/nitricOxideSynthaseStoichiometry.tsv b/data/modelCuration/nitricOxideSynthaseStoichiometry.tsv new file mode 100644 index 000000000..a4ba8cd93 --- /dev/null +++ b/data/modelCuration/nitricOxideSynthaseStoichiometry.tsv @@ -0,0 +1,2 @@ +entity field before after +MAR02023 metabolites MAM01365c:-1.0;MAM01588c:1.0;MAM02040c:2.0;MAM02554c:2.0;MAM02555c:-2.0;MAM02609c:1.0;MAM02630c:-2.0 MAM01365c:-2.0;MAM01588c:2.0;MAM02039c:-1.0;MAM02040c:4.0;MAM02554c:3.0;MAM02555c:-3.0;MAM02609c:2.0;MAM02630c:-4.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 59af48275..a749736f0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -203333,13 +203333,14 @@ - id: MAR02023 - name: L-Arginine, NADPH:Oxygen Oxidoreductase (Nitric-Oxide-Forming) - metabolites: !!omap - - MAM01365c: -1.0 - - MAM01588c: 1.0 - - MAM02040c: 2.0 - - MAM02554c: 2.0 - - MAM02555c: -2.0 - - MAM02609c: 1.0 - - MAM02630c: -2.0 + - MAM01365c: -2.0 + - MAM01588c: 2.0 + - MAM02039c: -1.0 + - MAM02040c: 4.0 + - MAM02554c: 3.0 + - MAM02555c: -3.0 + - MAM02609c: 2.0 + - MAM02630c: -4.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000007171 or ENSG00000089250 or ENSG00000164867 From ed75b1cfe3b00a2ba6cd31d6e7e7ab6cd30a3208 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 10:43:25 +0100 Subject: [PATCH 11/44] doc: literature registry rows for the aflatoxin B1 aldehyde reductases #1153 --- literature/registry.md | 2 ++ literature/registry.tsv | 4 +++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/literature/registry.md b/literature/registry.md index 5b79ea6ff..5f79a29b7 100644 --- a/literature/registry.md +++ b/literature/registry.md @@ -75,6 +75,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Grimminger F et al. (1993). A double-blind, randomized, placebo-controlled trial of n-3 fatty acid based lipid infusion in acute, extended guttate psoriasis. *The Clinical Investigator*. [doi:10.1007/bf00184491](https://doi.org/10.1007/bf00184491) | Homo sapiens | | `MAR02550` | In a 10-day trial of 20 psoriasis patients given n-3 or n-6 lipid infusions, ionophore-stimulated neutrophils generated leukotrienes; with the n-3 emulsion, LTA5 was measured as non-enzymatic degradation products (HPLC/UV). The non-enzymatic origin is assumed from the products, and the products were not identified by structure. | Results; Fig. 3 legend (p. 4, 7) | clinical, metabolite measurement | full text | Human-GEM#1173 | | Grishin A, Caplan M (1998). ATP1AL1, a Member of the Non-gastric H,K-ATPase Family, Functions as a Sodium Pump. *Journal of Biological Chemistry*. [doi:10.1074/jbc.273.43.27772](https://doi.org/10.1074/jbc.273.43.27772) | Homo sapiens | ATP12A, ATP4B | | In HEK 293 cells expressing ATP1AL1 (ATP12A) with the gastric H,K-ATPase beta subunit, Na+ content was lower and a Na+ efflux inhibited only by 1 mM ouabain appeared; 86Rb+ influx matched this efflux, so the authors conclude the pair mediates mainly Na+,K+ exchange rather than H+,K+ exchange. One heterologous cell system with the gastric beta subunit; the in vivo partner is not shown. | Abstract | expression, enzyme assay | abstract | Human-GEM#1169 | | Grootveld M, Halliwell B (1987). Measurement of allantoin and uric acid in human body fluids. A potential index of free-radical reactions in vivo?. *Biochemical Journal*. [doi:10.1042/bj2430803](https://doi.org/10.1042/bj2430803), [PMID:3663100](https://pubmed.ncbi.nlm.nih.gov/3663100/) | Homo sapiens | | | The paper describes methods for measuring uric acid and allantoin in human body fluids and reports their concentrations in human serum and synovial fluid, and the authors suggest that changes in allantoin concentration may index free-radical reactions in vivo. That radical attack on uric acid yields allantoin is cited from earlier work, not shown here. | Abstract | metabolite measurement | abstract | Human-GEM#1147 | +| Guengerich FP et al. (2001). Reduction of Aflatoxin B1 Dialdehyde by Rat and Human Aldo-keto Reductases. *Chemical Research in Toxicology*. [doi:10.1021/tx010005p](https://doi.org/10.1021/tx010005p), [PMID:11409944](https://pubmed.ncbi.nlm.nih.gov/11409944/) | Homo sapiens;Rattus norvegicus | AKR7A2, AKR7A3 | `MAR07025`, `MAR07026`, `MAR07027`, `MAR07028` | Rat and human aflatoxin B1 aldehyde reductase isozymes reduced the dialdehyde of aflatoxin B1 to the dialcohol with NADPH. Two monoalcohols formed: the monoalcohol reduced at C-8 appeared first and was reduced further to the dialcohol, while the C-6a monoalcohol formed but was not reduced to the dialcohol quickly. Limits: abstract read only; the abstract does not say which human isozyme was assayed, and the measured kinetic constants did not fit a simple kinetic model | Abstract | enzyme assay | abstract | Human-GEM#1153 | | Gustafsson J et al. (2023). Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. *Proceedings of the National Academy of Sciences*. [doi:10.1073/pnas.2217868120](https://doi.org/10.1073/pnas.2217868120), [PMID:36719923](https://pubmed.ncbi.nlm.nih.gov/36719923/) | Homo sapiens | | `MAR00015`, `MAR00016`, `MAR00017` | ftINIT builds context-specific models from pooled single-cell or bulk RNA-seq; with the mask used in this study, reactions without gene rules (spontaneous, exchange, transport and 52 custom reactions for protein generation and metabolite pooling) are left out of the optimization and always kept in the final model, except in the Metabolic Atlas models. | Materials and Methods: ftINIT | model | full text | animal-GEM | | Haapalainen AM et al. (2007). Crystallographic and Kinetic Studies of Human Mitochondrial Acetoacetyl-CoA Thiolase: The Importance of Potassium and Chloride Ions for Its Structure and Function,. *Biochemistry*. [doi:10.1021/bi6026192](https://doi.org/10.1021/bi6026192), [PMID:17371050](https://pubmed.ncbi.nlm.nih.gov/17371050/) | Homo sapiens | ACAT1 | `MAR03206` | Kinetic measurements on human mitochondrial acetoacetyl-CoA thiolase (T2, ACAT1) show thiolytic degradation of acetoacetyl-CoA and of 2-methylacetoacetyl-CoA with comparable kcat/Km, and turnover numbers for both substrates rise about 3-fold when KCl goes from 0 to 40 mM. Crystal structures of the apo and CoA-bound forms locate the potassium site near the CoA and catalytic sites and attribute the 2-methyl-branched substrate tolerance to the Phe325-Pro326 dipeptide. | Abstract | enzyme assay, structure | abstract | animal-GEM | | Haber H et al. (1996). Plasma and Urine Salsolinol in Humans: Effect of Acute Ethanol Intake on the Enantiomeric Composition of Salsolinol. *Alcoholism: Clinical and Experimental Research*. [doi:10.1111/j.1530-0277.1996.tb01049.x](https://doi.org/10.1111/j.1530-0277.1996.tb01049.x) | Homo sapiens | | `MAR06734`, `MAR06738` | GC-MS enantiomer analysis in urine and plasma of 24 subjects found salsolinol racemic in healthy subjects, with no change in enantiomer ratio after 1 g/kg ethanol, contrary to earlier HPLC reports of predominant R in urine. This argues against an enantioselective enzymatic route in these subjects; total salsolinol output rose in only five subjects. | Abstract | metabolite measurement, clinical | abstract | Human-GEM#1173 | @@ -100,6 +101,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Kemp S, Wanders RJA (2007). X-linked adrenoleukodystrophy: Very long-chain fatty acid metabolism, ABC half-transporters and the complicated route to treatment. *Molecular Genetics and Metabolism*. [doi:10.1016/j.ymgme.2006.10.001](https://doi.org/10.1016/j.ymgme.2006.10.001), [PMID:17092750](https://pubmed.ncbi.nlm.nih.gov/17092750/) | Homo sapiens | ABCD1 | `MAR02407`, `MAR02509` | This review states that X-linked adrenoleukodystrophy is caused by mutations in ABCD1, encoding the peroxisomal ABC half-transporter ALDP, and that ALDP mutations raise very-long-chain fatty acid levels and reduce peroxisomal VLCFA beta-oxidation; it also notes that overexpression of the related half-transporter ALDRP corrects the biochemical defect in patient cells and in Abcd1 knockout mice. | Abstract | review | abstract | animal-GEM | | Kiema TR et al. (2014). The crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase (T1): insight into the reaction mechanism of its thiolase and thioesterase activities. *Acta Crystallographica Section D Biological Crystallography*. [doi:10.1107/s1399004714023827](https://doi.org/10.1107/s1399004714023827), [PMID:25478839](https://pubmed.ncbi.nlm.nih.gov/25478839/) | Homo sapiens | ACAA2 | `MAR03885` | Crystal structures of human mitochondrial T1 (ACAA2), apo and with CoA at 2.0 Å, show a tetramer; in solution T1 has low acyl-CoA thioesterase activity on fatty acyl-CoAs, fastest with butyryl-CoA, and significant biosynthetic (condensing) thiolase activity that the authors predict to be physiologically important. | Abstract | structure, enzyme assay | abstract | animal-GEM | | Kim J et al. (2008). Decyanation of vitamin B12 by a trafficking chaperone. *Proceedings of the National Academy of Sciences*. [doi:10.1073/pnas.0805989105](https://doi.org/10.1073/pnas.0805989105), [PMID:18779575](https://pubmed.ncbi.nlm.nih.gov/18779575/) | Homo sapiens | MMACHC | `MAR08613` | Human MMACHC (cblC) is shown to catalyse reductive decyanation of cyanocobalamin, using electrons passed from NADPH through cytosolic flavoprotein oxidoreductases to cleave the cobalt-carbon bond and release cyanide, giving base-off cob(II)alamin that can be assimilated into methylcobalamin and adenosylcobalamin. The authors relate this to cblC patient fibroblasts responding poorly to cyanocobalamin while showing partial metabolic correction with aquocobalamin. | Abstract | enzyme assay, clinical | abstract | Human-GEM#1149 | +| Knight LP et al. (1999). cDNA cloning, expression and activity of a second human aflatoxin B1-metabolizing member of the aldo-keto reductase superfamily, AKR7A3. *Carcinogenesis*. [doi:10.1093/carcin/20.7.1215](https://doi.org/10.1093/carcin/20.7.1215), [PMID:10383892](https://pubmed.ncbi.nlm.nih.gov/10383892/) | Homo sapiens | AKR7A3, AKR7A2 | `MAR07025`, `MAR07026`, `MAR07027`, `MAR07028` | Cloned AKR7A3 from an adult human liver cDNA library and expressed recombinant rat AKR7A1 and human AKR7A3 in E. coli; both reduced model carbonyl compounds, and liquid chromatography with electrospray mass spectrometry confirmed the NADPH-dependent formation of aflatoxin B1 dialcohol by AKR7A3. The abstract describes the rat AKR7A1 and human AKR7A2 enzymes as NADPH-dependent and as forming the dialcohol from the aflatoxin B1 dihydrodiol. Limits: abstract read only; recombinant proteins | Abstract | enzyme assay | abstract | Human-GEM#1153 | | Knoth J et al. (1981). Stoichiometry of hydrogen ion-linked dopamine transport in chromaffin granule ghosts. *Biochemistry*. [doi:10.1021/bi00526a016](https://doi.org/10.1021/bi00526a016) | Bos taurus | | `MAR07633`, `MAR07635`, `MAR07636`, `MAR07637`, `MAR07681`, `MAR07736`, `MAR07737`, `MAR07738` | Bovine chromaffin granule ghosts take up dopamine with a stoichiometry of two H+ per dopamine. Other amines and acetylcholine are covered only by analogy; not human. | Results and Discussion (p. 6625) | metabolite measurement | full text | Human-GEM#1173 | | Körner C et al. (1999). Decreased availability of GDP-l-fucose in a patient with LAD II with normal GDP-d-mannose dehydratase and FX protein activities. *Journal of Leukocyte Biology*. [doi:10.1002/jlb.66.1.95](https://doi.org/10.1002/jlb.66.1.95) | Homo sapiens | GMDS, TSTA3 | `MAR08768` | A newly identified leukocyte adhesion deficiency type II patient had severe hypofucosylation, yet cytosolic extracts of the patient's leukocytes and fibroblasts made GDP-L-fucose from GDP-D-mannose normally in vitro, and the GDP-mannose 4,6-dehydratase and FX protein (TSTA3) transcripts were normal in amount with no coding mutations. The authors conclude that the main GDP-L-fucose synthesis pathway can be intact in this disorder, contrary to an earlier report (Sturla 1998); the paper does not measure FX protein enzymology beyond the extract assay. | Abstract | enzyme assay, expression, clinical | abstract | Human-GEM | | Korotkova N, Lidstrom ME (2004). MeaB Is a Component of the Methylmalonyl-CoA Mutase Complex Required for Protection of the Enzyme from Inactivation. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m312852200](https://doi.org/10.1074/jbc.m312852200), [PMID:14734568](https://pubmed.ncbi.nlm.nih.gov/14734568/) | Methylobacterium extorquens | meaB | | In Methylobacterium extorquens AM1, the growth defect of a meaB mutant comes from an inactive methylmalonyl-CoA mutase rather than from a lack of adenosylcobalamin, since double mutants blocked in R-methylmalonyl-CoA or adenosylcobalamin synthesis retain active mutase; purified MeaB forms a complex with the purified mutase and stimulates its activity in vitro, consistent with protection of the mutase from irreversible inactivation during catalysis. | Abstract | enzyme assay, knockout phenotype | abstract | Human-GEM#1156 | diff --git a/literature/registry.tsv b/literature/registry.tsv index 21dfde28f..663fe6cb7 100644 --- a/literature/registry.tsv +++ b/literature/registry.tsv @@ -178,7 +178,7 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1085/jgp.114.3.429 Lu CC, Hilgemann DW 1999 Gat1 (Gaba:Na+:Cl−) Cotransport Function The Journal of General Physiology Xenopus laevis (expression system) SLC6A1 MAR09613 Giant membrane patches from Xenopus oocytes expressing GAT1 gave reversal potentials consistent with a stoichiometry of 1 GABA : 2 Na+ : 1 Cl-. Expression-system study; the species of the GAT1 clone is not stated in the abstract. Abstract; Fig. 6 enzyme assay;expression full text Human-GEM#1173 10.1124/mol.58.6.1341 Marill J et al. 2000 Identification of Human Cytochrome P450s Involved in the Formation of All-trans-Retinoic Acid Principal Metabolites Molecular Pharmacology Homo sapiens CYP3A7;CYP3A5;CYP2C18;CYP2C8;CYP3A4;CYP2C9;CYP2B6;CYP2A6;CYP4A11;CYP1A1 MAR06700;MAR06701 Human liver microsomes and cDNA-expressed P450s formed 4-OH-RA and 4-oxo-RA mainly via CYP3A7, then CYP3A5, 2C8, 2C18, 3A4 and 2C9 (4-OH-RA by expressed P450s, ranked by Vmax/Km); CYP2B6 and 2A6 correlated with formation in liver microsomes. CYP26 enzymes and CYP2S1 are not among the P450s tested. Abstract enzyme assay;expression abstract Human-GEM#1169;Human-GEM#1118;Human-GEM#1163 10.1172/jci10902 Schwarz M et al. 2000 The bile acid synthetic gene 3β-hydroxy-Δ5-C27-steroid oxidoreductase is mutated in progressive intrahepatic cholestasis Journal of Clinical Investigation Homo sapiens;Mus musculus HSD3B7 MAR01796 Expression cloning gave a microsomal liver C27 3beta-HSD (HSD3B7) that acted on four 7alpha-hydroxylated sterols when transfected into cultured cells but not on C19/C21 steroids; a 2-bp deletion in HSD3B7 in a patient with neonatal cholestasis abolished activity. Cell-transfection assays; mouse used for mRNA regulation, human for the gene and the patient mutation. Abstract enzyme assay;clinical;expression abstract Human-GEM#1174 -10.5281/zenodo.3583004 Robinson JL et al. 2019 Supplementary data and scripts for \"An Atlas of Human Metabolism\" Zenodo Homo sapiens genome-wide Zenodo dataset (Human1_Publication_Data_Scripts.zip) with the models, data and scripts of the Human1 paper (tINIT GEMs, ecGEMs and others); the draft cites the script compare_gene_essentiality_results.m for the statement that Human1 predicted genes absent from a context model as non-essential. The script was not opened here, so that statement is taken from the draft. Zenodo record description model secondary Human-GEM#1175 +10.5281/zenodo.3583004 Robinson JL et al. 2019 "Supplementary data and scripts for \""An Atlas of Human Metabolism\""" Zenodo Homo sapiens genome-wide Zenodo dataset (Human1_Publication_Data_Scripts.zip) with the models, data and scripts of the Human1 paper (tINIT GEMs, ecGEMs and others); the draft cites the script compare_gene_essentiality_results.m for the statement that Human1 predicted genes absent from a context model as non-essential. The script was not opened here, so that statement is taken from the draft. Zenodo record description model secondary Human-GEM#1175 10.1007/bf03226377 Banoglu E et al. 2001 Hepatic microsomal metabolism of indole to indoxyl, a precursor of indoxyl sulfate European Journal of Drug Metabolism and Pharmacokinetics Rattus norvegicus CYP2E1 MAR10461 Rat liver microsomes with an NADPH-generating system oxidised indole to indoxyl (measured as indigo) with apparent Km 0.85 mM; inhibitor and inducer experiments showed P450 rather than FMO activity, and activity tracked CYP2E1 activity, so the authors conclude CYP2E1 is the major isoform. Rat microsomes only, no human enzyme tested. Abstract enzyme assay abstract Human-GEM#1173 10.1016/j.abb.2006.04.013 Fraisl P et al. 2006 A novel mammalian bubblegum-related acyl-CoA synthetase restricted to testes and possibly involved in spermatogenesis Archives of Biochemistry and Biophysics Homo sapiens; Mus musculus ACSBG2 MAR00249;MAR02957 A newly characterised membrane-associated acyl-CoA synthetase (BGR, ACSBG2) showed activity on long- and very long-chain fatty acids; its human mRNA was detected only in testis, and mouse Bgr was found in testis germ and Sertoli cells. The abstract does not name stearate, so it does not show activity on that substrate. Abstract enzyme assay;expression abstract Human-GEM#1169 10.1016/j.jpba.2012.02.002 de los Ángeles Juricic M et al. 2012 Salsolinol and isosalsolinol: Condensation products of acetaldehyde and dopamine. Separation of their enantiomers in the presence of a large excess of dopamine Journal of Pharmaceutical and Biomedical Analysis in vitro MAR06734;MAR06738 An analytical methods paper: HPLC, NMR and MS showed commercial salsolinol contains about 10% isosalsolinol, and an HPLC method separates the (S)- and (R)-salsolinol enantiomers in the presence of excess dopamine. The condensation of dopamine with acetaldehyde in vitro, the pyruvate route and a putative (R)-salsolinol synthase are stated only as background (suggested or postulated), not shown. Abstract; Introduction (background statements) metabolite measurement full text Human-GEM#1173 @@ -231,3 +231,5 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1021/jf0210066 Herraiz T 2003 L-tryptophan reacts with naturally occurring and food-occurring phenolic aldehydes to give phenolic tetrahydro-beta-carboline alkaloids: activity as antioxidants and free radical scavengers Journal of Agricultural and Food Chemistry in vitro (chemistry) Benzaldehyde and several phenolic aldehydes condensed with L-tryptophan in aqueous acid (heat needed for all but benzaldehyde) to give tetrahydro-beta-carboline-3-carboxylic acids as cis and trans isomers. The study shows aldehyde condensation only: the product is the tetrahydro acid, not the aromatic beta-carboline, and tryptophan without an aldehyde was not tested. Abstract metabolite measurement full text Human-GEM#1173;Human-GEM#1133 10.1016/s0945-053x(02)00071-9 12475640 Wang C et al. 2002 The third activity for lysyl hydroxylase 3: galactosylation of hydroxylysyl residues in collagens in vitro Matrix Biology Homo sapiens PLOD3 MAR06984 Recombinant human lysyl hydroxylase 3 transfers galactose to hydroxylysyl residues in collagen in vitro, in addition to its hydroxylase and glucosyltransferase activities. Abstract enzyme assay abstract Human-GEM#1174 10.1128/mcb.02085-07 19075007 Schegg B et al. 2009 Core Glycosylation of Collagen Is Initiated by Two β(1-O)Galactosyltransferases Molecular and Cellular Biology Homo sapiens COLGALT1;COLGALT2;PLOD3 MAR06984 GLT25D1 and GLT25D2 are the β(1-O)galactosyltransferases of collagen glycosylation; no galactosyltransferase activity was detected for lysyl hydroxylase 3. Abstract enzyme assay abstract Human-GEM#1174 +10.1021/tx010005p 11409944 Guengerich FP et al. 2001 Reduction of Aflatoxin B1 Dialdehyde by Rat and Human Aldo-keto Reductases Chemical Research in Toxicology Homo sapiens;Rattus norvegicus AKR7A2;AKR7A3 MAR07025;MAR07026;MAR07027;MAR07028 Rat and human aflatoxin B1 aldehyde reductase isozymes reduced the dialdehyde of aflatoxin B1 to the dialcohol with NADPH. Two monoalcohols formed: the monoalcohol reduced at C-8 appeared first and was reduced further to the dialcohol, while the C-6a monoalcohol formed but was not reduced to the dialcohol quickly. Limits: abstract read only; the abstract does not say which human isozyme was assayed, and the measured kinetic constants did not fit a simple kinetic model Abstract enzyme assay abstract Human-GEM#1153 +10.1093/carcin/20.7.1215 10383892 Knight LP et al. 1999 cDNA cloning, expression and activity of a second human aflatoxin B1-metabolizing member of the aldo-keto reductase superfamily, AKR7A3 Carcinogenesis Homo sapiens AKR7A3;AKR7A2 MAR07025;MAR07026;MAR07027;MAR07028 Cloned AKR7A3 from an adult human liver cDNA library and expressed recombinant rat AKR7A1 and human AKR7A3 in E. coli; both reduced model carbonyl compounds, and liquid chromatography with electrospray mass spectrometry confirmed the NADPH-dependent formation of aflatoxin B1 dialcohol by AKR7A3. The abstract describes the rat AKR7A1 and human AKR7A2 enzymes as NADPH-dependent and as forming the dialcohol from the aflatoxin B1 dihydrodiol. Limits: abstract read only; recombinant proteins Abstract enzyme assay abstract Human-GEM#1153 From fde78f34e0597d5ef1b71dccffe5efc9ec56a832 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 10:43:33 +0100 Subject: [PATCH 12/44] doc: describe the tables of the aflatoxin, diol epoxide and nitric oxide synthase curation #1153 --- data/modelCuration/README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index e4ef5d769..99013ccf9 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -46,3 +46,6 @@ This directory contains curation-related data files that support changes to the - `rxnFromHuman1Curation.tsv`: per-entity table of the change "rxnFrom on the reactions added in the Human1 curation" (`code/modelCuration/applyCurationTable.py`). Static dumps of external sources that were kept here during the Human1 series (SwissProt / Cell Atlas / DeepLoc2 subcellular locations, Rhea reaction associations, and metabolite SMILES/InChI) have been removed for the Human2 release. They had gone stale and are better queried fresh from the source when needed. They remain in the git history and in the last Human1 release, [v1.19.0](https://github.com/SysBioChalmers/Human-GEM/releases/tag/v1.19.0). +- `aflatoxinDialdehydeReductions.tsv`: per-entity table of the change "aflatoxin B1 dialdehyde reductions take NADPH" (`code/modelCuration/applyCurationTable.py`). +- `dibenzoPyreneDiolEpoxide.tsv`: per-entity table of the change "formula of the dibenzo[a,l]pyrene diol epoxide and the proton of its formation" (`code/modelCuration/applyCurationTable.py`). +- `nitricOxideSynthaseStoichiometry.tsv`: per-entity table of the change "stoichiometry of the arginine nitric oxide synthase reaction" (`code/modelCuration/applyCurationTable.py`). From 137653aee68f70c9ff5f6b70e0a307b8407028f2 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 10:52:02 +0100 Subject: [PATCH 13/44] doc: registry rows for the papers cited by MAR06639, and its replacement of MAR01506 MAR06639 cites three LRAT papers that had no row, and the Mondal 2000 row named MAR01506, which was merged into MAR06639 and deprecated. #1149 --- literature/registry.md | 5 ++++- literature/registry.tsv | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/literature/registry.md b/literature/registry.md index 5f79a29b7..c7cd94715 100644 --- a/literature/registry.md +++ b/literature/registry.md @@ -19,6 +19,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Binzak BA et al. (2001). Cloning of Dimethylglycine Dehydrogenase and a New Human Inborn Error of Metabolism, Dimethylglycine Dehydrogenase Deficiency. *The American Journal of Human Genetics*. [doi:10.1086/319520](https://doi.org/10.1086/319520) | Homo sapiens | DMGDH | `MAR04700` | DMGDH is described as a mitochondrial matrix enzyme converting dimethylglycine to sarcosine with FAD and folate; one adult patient with raised dimethylglycine carried a homozygous H109R change that inactivated the enzyme on expression. One patient; the mitochondrial location is stated as background. | Abstract | clinical, metabolite measurement | abstract | Human-GEM#1173 | | Birringer M et al. (2002). Identities and Differences in the Metabolism of Tocotrienols and Tocopherols in HepG2 Cells. *The Journal of Nutrition*. [doi:10.1093/jn/131.10.3113](https://doi.org/10.1093/jn/131.10.3113), [PMID:12368403](https://pubmed.ncbi.nlm.nih.gov/12368403/) | Homo sapiens | | | In HepG2 cells alpha- and gamma-tocotrienol were degraded by omega- then beta-oxidation of the side chain to carboxychromanols; the intermediate with the original side-chain double bond (CMBHC) was not detected, so auxiliary enzymes as for unsaturated fatty acids are implied. One cell line; no genes tested. | Abstract | metabolite measurement | abstract | Human-GEM#1173 | | Blanco A et al. (1976). Properties of the testicular lactate dehydrogenase isoenzyme. *Biochemical Journal*. [doi:10.1042/bj1530165](https://doi.org/10.1042/bj1530165) | Mus musculus;Columba livia;Homo sapiens;Bos taurus;Oryctolagus cuniculus | LDHC | `MAR05351`, `MAR11476`, `MAR11479` | LDH-X (LDHC) from mouse, pigeon and in sperm lysates of man, bull and rabbit converted 2-oxobutanoate and 2-oxopentanoate better than LDH 1 and LDH 5. Only the mouse enzyme used the branched 2-oxo acids well; pigeon, bull, rabbit and human LDH-X used them very poorly (Table 2), so branched-chain activity is not shown for human LDHC (see 10.1530/jrf.0.0550101). | Abstract; Table 2 (p. 168) | enzyme assay | full text | Human-GEM#1105, Human-GEM#1106 | +| Bok D et al. (2003). Purification and Characterization of a Transmembrane Domain-Deleted Form of Lecithin Retinol Acyltransferase. *Biochemistry*. [doi:10.1021/bi0342416](https://doi.org/10.1021/bi0342416), [PMID:12755610](https://pubmed.ncbi.nlm.nih.gov/12755610/) | multiple | LRAT | `MAR06639` | A truncated LRAT without its transmembrane ends, expressed in E. coli with a His tag and purified, was catalytically active and processed all-trans-retinol at least ten times more efficiently than 11-cis-retinol; it forms dimers, as native LRAT does. Limits: abstract read only; the abstract does not name the species of the LRAT gene, so the organism is recorded as multiple; recombinant truncated protein extracted with detergent | Abstract | enzyme assay | abstract | Human-GEM#1149 | | Bordbar A et al. (2011). iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. *BMC Systems Biology*. [doi:10.1186/1752-0509-5-110](https://doi.org/10.1186/1752-0509-5-110) | Homo sapiens | genome-wide | `MAR11318` | Proteomics-based reconstruction of mature erythrocyte metabolism with 281 enzymes, curated from literature and functionally tested; it is a model, not a measurement of any single transport step. The abstract says nothing about a proton channel or proton transport. | Abstract | model, expression | abstract | Human-GEM#1071 | | Brunk E et al. (2018). Recon3D enables a three-dimensional view of gene variation in human metabolism. *Nature Biotechnology*. [doi:10.1038/nbt.4072](https://doi.org/10.1038/nbt.4072) | Homo sapiens | genome-wide | | Presents the Recon3D human metabolic reconstruction (3,288 open reading frames, 13,543 reactions, 4,140 unique metabolites, 12,890 protein structures) as a computational model; it is a source model, not an experiment, so a reaction taken from it carries no measurement unless the reaction has its own reference. | Abstract | model | abstract | Human-GEM#1173, Human-GEM#1071 | | Burgos C et al. (1979). Substrate specificity of the lactate dehydrogenase isoenzyme C4 from human spermatozoa and a possible selective assay. *Reproduction*. [doi:10.1530/jrf.0.0550101](https://doi.org/10.1530/jrf.0.0550101) | Homo sapiens | LDHC | `MAR05351`, `MAR11476`, `MAR11479` | Human sperm lysates (LDH C4 identified by zymogram) were active with pyruvate, 2-oxobutanoate, 2-oxopentanoate and 2-oxohexanoate but showed no activity with the branched 2-oxo acids 2-oxo-3-methylbutanoate, 2-oxo-3-methylpentanoate and 2-oxo-4-methylpentanoate that LDH C4 of other species uses. Supports LDHC on the straight-chain reaction (MAR05351) and contradicts it on the branched ones (MAR11476, MAR11479); see also 10.1042/bj1530165. | Results (p. 101, 104) | enzyme assay | full text | Human-GEM#1105, Human-GEM#1106, Human-GEM#1169 | @@ -125,6 +126,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Longo N et al. (2016). Carnitine transport and fatty acid oxidation. *Biochimica et Biophysica Acta (BBA) - Molecular Cell Research*. [doi:10.1016/j.bbamcr.2016.01.023](https://doi.org/10.1016/j.bbamcr.2016.01.023), [PMID:26828774](https://pubmed.ncbi.nlm.nih.gov/26828774/) | Homo sapiens | SLC22A5 | | Review: normal circulating carnitine is 25-50 µM (0-8 µM in primary carnitine deficiency); cells accumulate carnitine and kidneys reabsorb it through the high-affinity carnitine transporter OCTN2 (SLC22A5), and inborn errors of carnitine synthesis usually leave plasma carnitine normal. | Abstract; Introduction | review | full text | Human-GEM#1118 | | Lu CC, Hilgemann DW (1999). Gat1 (Gaba:Na+:Cl−) Cotransport Function. *The Journal of General Physiology*. [doi:10.1085/jgp.114.3.429](https://doi.org/10.1085/jgp.114.3.429) | Xenopus laevis (expression system) | SLC6A1 | `MAR09613` | Giant membrane patches from Xenopus oocytes expressing GAT1 gave reversal potentials consistent with a stoichiometry of 1 GABA : 2 Na+ : 1 Cl-. Expression-system study; the species of the GAT1 clone is not stated in the abstract. | Abstract; Fig. 6 | enzyme assay, expression | full text | Human-GEM#1173 | | Luthria DL et al. (1995). Double Bond Removal from Odd-numbered Carbons during Peroxisomal β-Oxidation of Arachidonic Acid Requires both 2,4-Dienoyl-CoA Reductase and Δ3,5,Δ2,4-Dienoyl-CoA Isomerase. *Journal of Biological Chemistry*. [doi:10.1074/jbc.270.23.13771](https://doi.org/10.1074/jbc.270.23.13771), [PMID:7775433](https://pubmed.ncbi.nlm.nih.gov/7775433/) | Rattus norvegicus | ECH1 | `MAR03460` | Incubating clofibrate-induced rat liver peroxisomes with [1-14C]4,7,10-hexadecatrienoate gave 2-trans-4,7,10-hexadecatetraenoate plus two isomers carrying a conjugated triene (UV maxima at 257, 267 and 277 nm) that the authors assign as 3,5,7,10-hexadecatetraenoate, and the matching accumulation of 2-trans-4,8,11,14-eicosapentaenoate from arachidonate without NADPH led them to conclude that removal of the odd-numbered double bonds of arachidonate needs NADPH-dependent 2,4-dienoyl-CoA reductase together with a delta-3,5,delta-2,4-dienoyl-CoA isomerase acting in the reverse direction. | Results (Fig. 2 radiochromatograms, Figs. 4 and 5 UV spectra) and Discussion with the proposed pathway (Fig. 8) | enzyme assay, metabolite measurement | full text | animal-GEM | +| MacDonald PN et al. (1988). A lecithin: Retinol acyltransferase activity in human and rat liver. *Biochemical and Biophysical Research Communications*. [doi:10.1016/s0006-291x(88)80818-0](https://doi.org/10.1016/s0006-291x(88)80818-0), [PMID:3178828](https://pubmed.ncbi.nlm.nih.gov/3178828/) | Homo sapiens;Rattus norvegicus | | `MAR06639` | Human and rat liver microsomes esterified retinol bound to cellular retinol-binding protein with phosphatidylcholine as the acyl donor, and transferred little or no acyl from lysophosphatidylcholine, phosphatidylethanolamine or phosphatidic acid; only the acyl group at the sn-1 position of phosphatidylcholine was transferred. Limits: abstract read only; microsomal preparations in vitro; the enzyme and its gene were not identified | Abstract | enzyme assay | abstract | Human-GEM#1149 | | Malatesta M et al. (2024). One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse. *Nature Communications*. [doi:10.1038/s41467-024-47466-3](https://doi.org/10.1038/s41467-024-47466-3), [PMID:38615009](https://pubmed.ncbi.nlm.nih.gov/38615009/) | Homo sapiens;Mus musculus | SHMT1, SHMT2 | `MAR06979`, `MAR01371`, `MAR20236` | Docking of a substrate to AlphaFold models of vitamin B6 enzymes, followed by experimental testing, showed that SHMT1 and SHMT2 catalyse the hydroxytrimethyllysine aldolase step of carnitine biosynthesis; a mouse threonine aldolase (Tha1) that humans lack does it more efficiently. The authors suggest that SHMT activity partly makes up for this gene loss in humans. | Abstract | enzyme assay, structure | abstract | Human-GEM#1174 | | Manuel Liaci A et al. (2026). Structural basis of signal peptide recognition by the signal peptidase complex. *Nature Communications*. [doi:10.1038/s41467-026-73423-3](https://doi.org/10.1038/s41467-026-73423-3), [PMID:42173868](https://pubmed.ncbi.nlm.nih.gov/42173868/) | Homo sapiens | SPCS1, SPCS2, SPCS3, SEC11A, SEC11C | `MAR06978`, `MAR08029` | A 2.6 Angstrom cryo-EM map of human SPC-A bound to a model signal peptide shows the c-region of the peptide in a hydrophobic luminal groove next to the active site, a narrow gate at the transition from c-region to h-region, and the h-region in a transmembrane window; substrate binding stabilises the N- and C-terminal helices of SEC11A that are unresolved in the apo structure. Molecular dynamics and AlphaFold modelling support this binding mode. | Abstract | structure, model | full text | Human-GEM#1157 | | Mao L et al. (1995). Mitochondrial β-Oxidation of 2-Methyl Fatty Acids in Rat Liver. *Archives of Biochemistry and Biophysics*. [doi:10.1006/abbi.1995.1389](https://doi.org/10.1006/abbi.1995.1389) | Rattus norvegicus | HADHA, HADHB, ACAA2 | `MAR06434`, `MAR06435`, `MAR06436`, `MAR06450`, `MAR06451`, `MAR06453`, `MAR06472`, `MAR06473`, `MAR06486`, `MAR06488` | Coupled rat liver mitochondria and purified enzymes: the trifunctional beta-oxidation complex hydrates, dehydrogenates and cleaves medium- and long-chain 2-methyl-branched substrates, whereas the matrix L-3-hydroxyacyl-CoA dehydrogenase and 3-ketoacyl-CoA thiolase are inactive with them. Rat only; no vitamin E carboxychromanol intermediate was tested, so the use for the tocotrienol rounds is an inference. | Abstract | enzyme assay | abstract | Human-GEM#1118, Human-GEM#1169, Human-GEM#1173 | @@ -143,7 +145,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Meotti FC et al. (2011). Urate as a Physiological Substrate for Myeloperoxidase. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m110.172460](https://doi.org/10.1074/jbc.m110.172460), [PMID:21266577](https://pubmed.ncbi.nlm.nih.gov/21266577/) | Homo sapiens | MPO | | Myeloperoxidase with hydrogen peroxide oxidised urate to 5-hydroxyisourate, which decayed mainly to allantoin; urate reduced MPO compound I and compound II with rate constants of 4.6e5 and 1.7e4 per molar per second and competed with chloride, and stimulated neutrophils in human plasma produced allantoin in an NADPH oxidase, MPO and superoxide dependent reaction. | Abstract | enzyme assay, metabolite measurement | abstract | Human-GEM#1147 | | Merickel A, Edwards RH (1995). Transport of histamine by vesicular monoamine transporter-2. *Neuropharmacology*. [doi:10.1016/0028-3908(95)00148-y](https://doi.org/10.1016/0028-3908(95)00148-y) | not stated | SLC18A2 | `MAR07633` | In a heterologous expression system VMAT2 took up 3H-histamine, which was also an inhibitor of serotonin transport by VMAT2 but not VMAT1; histamine did not displace 3H-reserpine, and reserpine blocked histamine transport much less potently than serotonin transport. Mutating serines in transmembrane domain 3 abolished histamine transport. Only VMAT2 was tested as a histamine carrier in this abstract; the species of the transporter is not given in the abstract and the VMAT1 result is inhibition-based, not a transport assay. | Abstract | enzyme assay | abstract | Human-GEM | | Miller EW et al. (2010). Aquaporin-3 mediates hydrogen peroxide uptake to regulate downstream intracellular signaling. *Proceedings of the National Academy of Sciences*. [doi:10.1073/pnas.1005776107](https://doi.org/10.1073/pnas.1005776107) | mammals | AQP3, AQP8, AQP1 | `MAR08408` | With a fluorescent H2O2 probe, AQP3 and AQP8 increased H2O2 uptake into mammalian cells, but AQP1 did not, and endogenous AQP3 level changed intracellular H2O2 and growth-factor signalling. The AQP1 negative is from overexpression in the cells tested (the draft cites HEK293); the abstract does not name the cell line. | Abstract | expression, metabolite measurement | abstract | Human-GEM#1169 | -| Mondal MS et al. (2000). Lecithin Retinol Acyltransferase Contains Cysteine Residues Essential for Catalysis. *Biochemistry*. [doi:10.1021/bi9929554](https://doi.org/10.1021/bi9929554), [PMID:10819989](https://pubmed.ncbi.nlm.nih.gov/10819989/) | Homo sapiens | LRAT | `MAR01501`, `MAR01506` | LRAT from human retinal pigment epithelium is highly sensitive to thiol-directed reagents; C161A and C168A mutants are virtually inactive, C182A and C208A keep most activity, and C161S retains a few percent with an aberrant pH-rate profile, so the authors conclude LRAT is a thiol acyltransferase with C161 as the likely nucleophile. | Abstract | enzyme assay | abstract | Human-GEM#1149, animal-GEM | +| Mondal MS et al. (2000). Lecithin Retinol Acyltransferase Contains Cysteine Residues Essential for Catalysis. *Biochemistry*. [doi:10.1021/bi9929554](https://doi.org/10.1021/bi9929554), [PMID:10819989](https://pubmed.ncbi.nlm.nih.gov/10819989/) | Homo sapiens | LRAT | `MAR01501`, `MAR06639` | LRAT from human retinal pigment epithelium is highly sensitive to thiol-directed reagents; C161A and C168A mutants are virtually inactive, C182A and C208A keep most activity, and C161S retains a few percent with an aberrant pH-rate profile, so the authors conclude LRAT is a thiol acyltransferase with C161 as the likely nucleophile. | Abstract | enzyme assay | abstract | Human-GEM#1149, animal-GEM | | Monks TJ et al. (1984). The mechanism of formation of o-bromophenol from bromobenzene.. *Drug Metabolism and Disposition*. [doi:10.1016/s0090-9556(25)07705-0](https://doi.org/10.1016/s0090-9556(25)07705-0), [PMID:6144485](https://pubmed.ncbi.nlm.nih.gov/6144485/) | Rattus norvegicus | | `MAR07049` | In liver microsomes from 3-methylcholanthrene-treated rats, a bromobenzene 2,3-dihydrodiol was isolated and the deuterium label of o-bromophenol was largely retained, with no isotope effect; this indicates formation via bromobenzene-2,3-oxide rather than direct oxygen insertion. The authors state the result does not exclude oxygen addition followed by an NIH shift, and the abstract does not address spontaneous versus enzymatic isomerisation of the oxide. | Abstract | enzyme assay, metabolite measurement | abstract | Human-GEM#1173 | | Montiel V et al. (2020). Inhibition of aquaporin-1 prevents myocardial remodeling by blocking the transmembrane transport of hydrogen peroxide. *Science Translational Medicine*. [doi:10.1126/scitranslmed.aay2176](https://doi.org/10.1126/scitranslmed.aay2176) | Homo sapiens;Mus musculus | AQP1 | `MAR08408` | Cardiac myocytes: AQP1 sits at the plasma membrane with NADPH oxidase-2, and its deletion or pore blockade inhibited H2O2 transport in mouse and human cells and rescued hypertrophy in iPSC-derived human engineered heart muscle; the authors conclude AQP1 mediates H2O2 entry in cardiomyocytes. Cardiomyocytes only; other cell types are not covered. | Abstract | knockout phenotype, localization | abstract | Human-GEM#1169 | | Moon YA, Horton JD (2003). Identification of Two Mammalian Reductases Involved in the Two-carbon Fatty Acyl Elongation Cascade. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m211684200](https://doi.org/10.1074/jbc.m211684200), [PMID:12482854](https://pubmed.ncbi.nlm.nih.gov/12482854/) | mammals | HSD17B12, TECR | `MAR03417`, `MAR03474`, `MAR03412`, `MAR03442` | Two mammalian enzymes of the microsomal fatty acyl elongation cycle were identified and characterised: the 3-ketoacyl-CoA reductase and the trans-2,3-enoyl-CoA reductase, acting in long- and very-long-chain elongation respectively. The abstract names no gene symbols; UniProt assigns these activities to HSD17B12 (Q53GQ0, EC 1.1.1.330) and TECR (Q9NZ01, EC 1.3.1.93), citing this paper as experimental evidence. | Abstract | enzyme assay | abstract | Human-GEM#1151 | @@ -186,6 +188,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Robinson JL et al. (2020). An atlas of human metabolism. *Science Signaling*. [doi:10.1126/scisignal.aaz1482](https://doi.org/10.1126/scisignal.aaz1482), [PMID:32209698](https://pubmed.ncbi.nlm.nih.gov/32209698/) | Homo sapiens | genome-wide | `MAR13082` | In the Human1 (Human-GEM) gene essentiality analysis, a gene counts as essential if its deletion impairs any of 57 basic metabolic tasks, biomass production among them, rather than growth alone; the authors state this reduces dependence on the biomass reaction formulation and hypothesise higher sensitivity. Predictions were made on five cell-line-specific models built with tINIT from CRISPR-screened cell lines (GBM, RPE1, HCT116, DLD1, HeLa) and compared with HMR2 and Recon3D. | Results: Prediction of metabolic task-essential genes in human cell lines; Fig. 4A | model, genetic screen | full text | animal-GEM | | Rodrigues JT et al. (2026). Structural conservation, functional decline: The fate of human OHCU decarboxylase. *Biochimie*. [doi:10.1016/j.biochi.2026.04.002](https://doi.org/10.1016/j.biochi.2026.04.002), [PMID:41956358](https://pubmed.ncbi.nlm.nih.gov/41956358/) | Homo sapiens | URAD | `MAR10116` | Recombinant human OHCU decarboxylase (URAD) is a well-folded alpha-helical protein closely similar to the zebrafish enzyme (52% sequence identity, RMSD below 0.8 Angstrom) but less stable, and in functional assays its catalytic activity is markedly lower than that of the zebrafish enzyme; molecular dynamics indicates different ligand binding and altered conformational flexibility in the human protein. | Abstract | enzyme assay, structure, model | abstract | Human-GEM#1147 | | Rokka A et al. (2009). Pxmp2 Is a Channel-Forming Protein in Mammalian Peroxisomal Membrane. *PLoS ONE*. [doi:10.1371/journal.pone.0005090](https://doi.org/10.1371/journal.pone.0005090), [PMID:19352492](https://pubmed.ncbi.nlm.nih.gov/19352492/) | Mus musculus | PXMP2 | | Liver peroxisomes from Pxmp2 knockout mice kept part of their permeability to small solutes in vitro and in vivo, lost 1.3 nS channel activity, and recombinant and native Pxmp2 formed a weakly cation-selective pore of about 1.4 nm; the authors conclude cofactors and ATP need specific transporters. Mouse and insect-cell expression, not human. | Abstract | knockout phenotype, enzyme assay | abstract | Human-GEM#1071 | +| Saari JC et al. (1989). Lecithin:Retinol Acyltransferase in Retinal Pigment Epithelial Microsomes. *Journal of Biological Chemistry*. [doi:10.1016/s0021-9258(18)81839-7](https://doi.org/10.1016/s0021-9258(18)81839-7), [PMID:2722792](https://pubmed.ncbi.nlm.nih.gov/2722792/) | Bos taurus | | `MAR06639` | Microsomes from retinal pigment epithelium made phosphatidylcholine from 1-palmitoyl lysophosphatidylcholine and fatty acyl-CoA, and this phosphatidylcholine served as the acyl donor for retinyl ester synthesis, which shows a lecithin:retinol acyltransferase activity; the acyl group is transferred from the 1 position of phosphatidylcholine, and the fatty acid at the 2 position matters for substrate recognition. Limits: abstract read only, and the species (bovine) is taken from the database indexing of the paper, not from the abstract; microsomes in vitro; no gene identified | Abstract | enzyme assay | abstract | Human-GEM#1149 | | Said HM (2004). Recent Advances in Carrier-Mediated Intestinal Absorption of Water-Soluble Vitamins. *Annual Review of Physiology*. [doi:10.1146/annurev.physiol.66.032102.144611](https://doi.org/10.1146/annurev.physiol.66.032102.144611) | Homo sapiens;mammals | | | Review of carrier-mediated intestinal absorption of water-soluble vitamins (ascorbate, biotin, folate, riboflavin, thiamin, pyridoxine), covering driving forces, molecular identity and regulation of the transporters. Cited as a reference of MAR06512 (FAD exchange); the abstract does not mention FAD transport and the four genes of that reaction are not transporters. | Abstract | review | abstract | Human-GEM#1173 | | Sakaki T et al. (2000). Dual metabolic pathway of 25-hydroxyvitamin D3 catalyzed by human CYP24. *European Journal of Biochemistry*. [doi:10.1046/j.1432-1327.2000.01680.x](https://doi.org/10.1046/j.1432-1327.2000.01680.x) | Homo sapiens | CYP24A1 | `MAR20224`, `MAR20225` | Human CYP24 expressed in E. coli with adrenodoxin and adrenodoxin reductase converted 25(OH)D3 and 1alpha,25(OH)2D3 along both a C-23 hydroxylation route (to the 26,23-lactone) and a C-24 route (via 24-oxo intermediates to tetranor-23(OH)D3), unlike rat CYP24 which lacked the C-23 route. Recombinant bacterial system only; vitamin D2 substrates not covered. | Abstract | enzyme assay | abstract | Human-GEM#1173, Human-GEM#1118, Human-GEM#1133, Human-GEM#1163 | | Samokyszyn VM et al. (2000). 4-Hydroxyretinoic Acid, a Novel Substrate for Human Liver Microsomal UDP-glucuronosyltransferase(s) and Recombinant UGT2B7. *Journal of Biological Chemistry*. [doi:10.1074/jbc.275.10.6908](https://doi.org/10.1074/jbc.275.10.6908) | Homo sapiens | UGT2B7 | | Human liver microsomes and recombinant UGT2B7 glucuronidated all-trans-retinoic acid, 4-hydroxy-retinoic acid and 4-hydroxy-retinyl acetate, with microsomal activity on 4-hydroxy-retinoic acid 6-fold that on retinoic acid; retinoic acid, 4-oxo- and 5,6-epoxy-retinoic acid gave carboxyl-linked glucuronides. The authors postulate a key role for UGT2B7. | Abstract | enzyme assay | abstract | Human-GEM#1118 | diff --git a/literature/registry.tsv b/literature/registry.tsv index 663fe6cb7..4103e1110 100644 --- a/literature/registry.tsv +++ b/literature/registry.tsv @@ -59,7 +59,7 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1038/s41467-023-40077-4 37468522 Mascarenhas R et al. 2023 Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B12 delivery and repair Nature Communications Homo sapiens MMAA;MMAB;MMUT A crystal structure of the human MMUT-MMAA assembly (two MMUT chains with two MMAA dimers) shows the MMUT B12 domain rotated about 180 degrees relative to free MMUT and exposed to solvent, with MMAA wedged between the substrate and B12 domains and the interconnecting belt partially disordered. Methylmalonic aciduria mutations at the interfaces (MMUT R228Q, R616C, R694W; MMAA R98G, R209S) reduce MMUT-stimulated GTPase activation and MMAA-gated AdoCbl transfer, supporting the relevance of the structure. Results: MMUT in the M2C2 complex; Fig. 3A structure;enzyme assay;clinical full text Human-GEM#1156 10.1016/j.ymgme.2017.11.002 29153845 McDonald MK et al. 2017 Identification of ABC transporters acting in vitamin B 12 metabolism in Caenorhabditis elegans Molecular Genetics and Metabolism Caenorhabditis elegans wht-6 MAR08614 A screen of 37 Caenorhabditis elegans ABC transporter mutants for methylmalonic acid excretion identified wht-6, which excreted more methylmalonic acid and incorporated less 14C-propionate while cystathionine excretion stayed normal, and the excretion was partly corrected by vitamin B12 in the medium; the authors propose wht-6, whose human ortholog belongs to the ABCG family, as a candidate mitochondrial cobalamin importer, the gene for which is not known. Abstract genetic screen;knockout phenotype;metabolite measurement abstract Human-GEM#1156 10.1074/jbc.m110.172460 21266577 Meotti FC et al. 2011 Urate as a Physiological Substrate for Myeloperoxidase Journal of Biological Chemistry Homo sapiens MPO Myeloperoxidase with hydrogen peroxide oxidised urate to 5-hydroxyisourate, which decayed mainly to allantoin; urate reduced MPO compound I and compound II with rate constants of 4.6e5 and 1.7e4 per molar per second and competed with chloride, and stimulated neutrophils in human plasma produced allantoin in an NADPH oxidase, MPO and superoxide dependent reaction. Abstract enzyme assay;metabolite measurement abstract Human-GEM#1147 -10.1021/bi9929554 10819989 Mondal MS et al. 2000 Lecithin Retinol Acyltransferase Contains Cysteine Residues Essential for Catalysis Biochemistry Homo sapiens LRAT MAR01501;MAR01506 LRAT from human retinal pigment epithelium is highly sensitive to thiol-directed reagents; C161A and C168A mutants are virtually inactive, C182A and C208A keep most activity, and C161S retains a few percent with an aberrant pH-rate profile, so the authors conclude LRAT is a thiol acyltransferase with C161 as the likely nucleophile. Abstract enzyme assay abstract Human-GEM#1149;animal-GEM +10.1021/bi9929554 10819989 Mondal MS et al. 2000 Lecithin Retinol Acyltransferase Contains Cysteine Residues Essential for Catalysis Biochemistry Homo sapiens LRAT MAR01501;MAR06639 LRAT from human retinal pigment epithelium is highly sensitive to thiol-directed reagents; C161A and C168A mutants are virtually inactive, C182A and C208A keep most activity, and C161S retains a few percent with an aberrant pH-rate profile, so the authors conclude LRAT is a thiol acyltransferase with C161 as the likely nucleophile. Abstract enzyme assay abstract Human-GEM#1149;animal-GEM 10.1074/jbc.m211684200 12482854 Moon YA, Horton JD 2003 Identification of Two Mammalian Reductases Involved in the Two-carbon Fatty Acyl Elongation Cascade Journal of Biological Chemistry mammals HSD17B12;TECR MAR03417;MAR03474;MAR03412;MAR03442 Two mammalian enzymes of the microsomal fatty acyl elongation cycle were identified and characterised: the 3-ketoacyl-CoA reductase and the trans-2,3-enoyl-CoA reductase, acting in long- and very-long-chain elongation respectively. The abstract names no gene symbols; UniProt assigns these activities to HSD17B12 (Q53GQ0, EC 1.1.1.330) and TECR (Q9NZ01, EC 1.3.1.93), citing this paper as experimental evidence. Abstract enzyme assay abstract Human-GEM#1151 10.1038/s41929-023-01087-z 38425362 Nicoll CR et al. 2024 In vitro construction of the COQ metabolon unveils the molecular determinants of coenzyme Q biosynthesis Nature Catalysis Homo sapiens COQ4;COQ8 MAR06906 Using ancestral sequence reconstruction to obtain soluble enzymes, the authors assembled the animal COQ biosynthetic pathway in vitro, assigned enzymes to steps that had been uncharacterised, and showed that the kinase COQ8 increases and streamlines coenzyme Q production in that reconstituted system. Abstract enzyme assay;phylogeny full text Human-GEM#1149 10.1093/oxfordjournals.molbev.a004123 11961098 Oda M et al. 2002 Loss of Urate Oxidase Activity in Hominoids and its Evolutionary Implications Molecular Biology and Evolution Homo sapiens UOX Sequencing of the Uox promoter, coding and intronic regions across primates confirmed that the gene is inactivated in humans and great apes by a single shared CGA to TGA nonsense mutation in exon 2, whereas the gibbon lineage was inactivated independently by a nonsense mutation at a different exon 2 CGA codon or by frameshifts in exon 3 or exon 5; substitutions in the CAAT box of functional primate Uox genes may also lower transcription. Abstract phylogeny;genome analysis abstract Human-GEM#1147 @@ -233,3 +233,6 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1128/mcb.02085-07 19075007 Schegg B et al. 2009 Core Glycosylation of Collagen Is Initiated by Two β(1-O)Galactosyltransferases Molecular and Cellular Biology Homo sapiens COLGALT1;COLGALT2;PLOD3 MAR06984 GLT25D1 and GLT25D2 are the β(1-O)galactosyltransferases of collagen glycosylation; no galactosyltransferase activity was detected for lysyl hydroxylase 3. Abstract enzyme assay abstract Human-GEM#1174 10.1021/tx010005p 11409944 Guengerich FP et al. 2001 Reduction of Aflatoxin B1 Dialdehyde by Rat and Human Aldo-keto Reductases Chemical Research in Toxicology Homo sapiens;Rattus norvegicus AKR7A2;AKR7A3 MAR07025;MAR07026;MAR07027;MAR07028 Rat and human aflatoxin B1 aldehyde reductase isozymes reduced the dialdehyde of aflatoxin B1 to the dialcohol with NADPH. Two monoalcohols formed: the monoalcohol reduced at C-8 appeared first and was reduced further to the dialcohol, while the C-6a monoalcohol formed but was not reduced to the dialcohol quickly. Limits: abstract read only; the abstract does not say which human isozyme was assayed, and the measured kinetic constants did not fit a simple kinetic model Abstract enzyme assay abstract Human-GEM#1153 10.1093/carcin/20.7.1215 10383892 Knight LP et al. 1999 cDNA cloning, expression and activity of a second human aflatoxin B1-metabolizing member of the aldo-keto reductase superfamily, AKR7A3 Carcinogenesis Homo sapiens AKR7A3;AKR7A2 MAR07025;MAR07026;MAR07027;MAR07028 Cloned AKR7A3 from an adult human liver cDNA library and expressed recombinant rat AKR7A1 and human AKR7A3 in E. coli; both reduced model carbonyl compounds, and liquid chromatography with electrospray mass spectrometry confirmed the NADPH-dependent formation of aflatoxin B1 dialcohol by AKR7A3. The abstract describes the rat AKR7A1 and human AKR7A2 enzymes as NADPH-dependent and as forming the dialcohol from the aflatoxin B1 dihydrodiol. Limits: abstract read only; recombinant proteins Abstract enzyme assay abstract Human-GEM#1153 +10.1021/bi0342416 12755610 Bok D et al. 2003 Purification and Characterization of a Transmembrane Domain-Deleted Form of Lecithin Retinol Acyltransferase Biochemistry multiple LRAT MAR06639 A truncated LRAT without its transmembrane ends, expressed in E. coli with a His tag and purified, was catalytically active and processed all-trans-retinol at least ten times more efficiently than 11-cis-retinol; it forms dimers, as native LRAT does. Limits: abstract read only; the abstract does not name the species of the LRAT gene, so the organism is recorded as multiple; recombinant truncated protein extracted with detergent Abstract enzyme assay abstract Human-GEM#1149 +10.1016/s0006-291x(88)80818-0 3178828 MacDonald PN et al. 1988 A lecithin: Retinol acyltransferase activity in human and rat liver Biochemical and Biophysical Research Communications Homo sapiens;Rattus norvegicus MAR06639 Human and rat liver microsomes esterified retinol bound to cellular retinol-binding protein with phosphatidylcholine as the acyl donor, and transferred little or no acyl from lysophosphatidylcholine, phosphatidylethanolamine or phosphatidic acid; only the acyl group at the sn-1 position of phosphatidylcholine was transferred. Limits: abstract read only; microsomal preparations in vitro; the enzyme and its gene were not identified Abstract enzyme assay abstract Human-GEM#1149 +10.1016/s0021-9258(18)81839-7 2722792 Saari JC et al. 1989 Lecithin:Retinol Acyltransferase in Retinal Pigment Epithelial Microsomes Journal of Biological Chemistry Bos taurus MAR06639 Microsomes from retinal pigment epithelium made phosphatidylcholine from 1-palmitoyl lysophosphatidylcholine and fatty acyl-CoA, and this phosphatidylcholine served as the acyl donor for retinyl ester synthesis, which shows a lecithin:retinol acyltransferase activity; the acyl group is transferred from the 1 position of phosphatidylcholine, and the fatty acid at the 2 position matters for substrate recognition. Limits: abstract read only, and the species (bovine) is taken from the database indexing of the paper, not from the abstract; microsomes in vitro; no gene identified Abstract enzyme assay abstract Human-GEM#1149 From b7be584c7467c671a2f3cd316b3a0a35915760ff Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:08:03 +0100 Subject: [PATCH 14/44] fix: count the vinyl ether carbons of the alkenyl ether lipids inside R The alkyl ether lipids put the whole chain in R, while the six alkenyl ether lipids wrote the two carbons of the vinyl ether out next to R, so the plasmanylethanolamine desaturase (MAR07601) came out short by C2H4. The alkenyl formulas now follow the alkyl convention, and the reactions among them stay balanced. The SMILES keep the drawn vinyl ether, the only place where the double bond is recorded. Generated by `code/modelCuration/applyCurationTable.py --table data/modelCuration/alkenylEtherLipidFormulas.tsv`. #1153 --- data/modelCuration/alkenylEtherLipidFormulas.tsv | 7 +++++++ model/Human-GEM.yml | 12 ++++++------ 2 files changed, 13 insertions(+), 6 deletions(-) create mode 100644 data/modelCuration/alkenylEtherLipidFormulas.tsv diff --git a/data/modelCuration/alkenylEtherLipidFormulas.tsv b/data/modelCuration/alkenylEtherLipidFormulas.tsv new file mode 100644 index 000000000..e9dda313e --- /dev/null +++ b/data/modelCuration/alkenylEtherLipidFormulas.tsv @@ -0,0 +1,7 @@ +entity field before after +MAM00222c formula C5H10O6PR C3H6O6PR +MAM00223c formula C7H15NO6PR C5H11NO6PR +MAM00224c formula C5H9O3R C3H5O3R +MAM00512c formula C6H8O4R2 C4H4O4R2 +MAM00627c formula C6H7O7PR2 C4H3O7PR2 +MAM02629c formula C8H14NO7PR2 C6H10NO7PR2 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index a749736f0..44f34c022 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -2972,21 +2972,21 @@ - name: 1-(1-alkenyl)-sn-glycero-3-phosphate - compartment: c - charge: 0.0 - - formula: C5H10O6PR + - formula: C3H6O6PR - metFrom: HMRdatabase - !!omap - id: MAM00223c - name: 1-(1-alkenyl)-sn-glycero-3-phosphoethanolamine - compartment: c - charge: 0.0 - - formula: C7H15NO6PR + - formula: C5H11NO6PR - metFrom: HMRdatabase - !!omap - id: MAM00224c - name: 1-(1-alkenyl)-sn-glycerol - compartment: c - charge: 0.0 - - formula: C5H9O3R + - formula: C3H5O3R - metFrom: HMRdatabase - !!omap - id: MAM00225c @@ -5961,7 +5961,7 @@ - name: 1-alkenyl-2-acylglycerol - compartment: c - charge: 0.0 - - formula: C6H8O4R2 + - formula: C4H4O4R2 - metFrom: HMRdatabase - !!omap - id: MAM00513c @@ -7158,7 +7158,7 @@ - name: 2-acyl-1-(1-alkenyl)-sn-glycero-3-phosphate - compartment: c - charge: -2.0 - - formula: C6H7O7PR2 + - formula: C4H3O7PR2 - metFrom: HMRdatabase - !!omap - id: MAM00628c @@ -31016,7 +31016,7 @@ - name: O-1-alk-1-enyl-2-acyl-sn-glycero-3-phosphoethanolamine - compartment: c - charge: 0.0 - - formula: C8H14NO7PR2 + - formula: C6H10NO7PR2 - metFrom: HMRdatabase - !!omap - id: MAM02630c From efd21e7be6a45b6a9709c52a07c063cc15425e0d Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:08:44 +0100 Subject: [PATCH 15/44] fix: exclude the reactions that join two conventions of R and X from the balance test Three reactions take a metabolite from one convention of the placeholder elements to another, so their two sides do not count the same atoms. They are listed by identifier with their reasons and audited on every run, like the lumped reactions. #1153 --- code/test/balanceTest.py | 50 +++++++++++++++++++++++------ code/test/unit/test_balance_test.py | 28 ++++++++++++++++ data/testResults/README.md | 2 ++ 3 files changed, 71 insertions(+), 9 deletions(-) diff --git a/code/test/balanceTest.py b/code/test/balanceTest.py index 433feeade..4c1fbee92 100644 --- a/code/test/balanceTest.py +++ b/code/test/balanceTest.py @@ -14,6 +14,9 @@ audited on every run, so an entry that the model no longer needs is reported rather than left to rot. +Three reactions that join two conventions of the placeholder elements are listed +by identifier in CONVENTION_BRIDGES and audited in the same way. + R and X are left as elements of their own, not ignored. A reaction that uses them is still expected to balance in them, and several do not, which is a finding rather than noise (#1153). @@ -62,6 +65,24 @@ "MAR07164": "RNA to a mixture of NMPs", } +# Reactions that join two bookkeeping conventions of the placeholder elements, +# so that the element counts of the two sides do not describe the same atoms and +# no elemental balance exists for them. Rewriting one convention would unbalance +# the reactions that use it, or discard structure that only that convention +# records. As with LUMPED_REACTIONS, a reaction that is merely unbalanced does +# not belong here. +CONVENTION_BRIDGES = { + # X is the whole protein with the residue inside it, as in the glycosylation + # and GPI networks; R2 writes the residue out, as in the other protein + # residues of the model. + "MAR07197": "[protein] (R2, residue written out) to [protein]-L-serine (X, residue inside X)", + "MAR07282": "[protein] (R2, residue written out) to [protein]-L-asparagine (X, residue inside X)", + # In the fatty acyl-CoA pool R starts after the carbonyl carbon; in the fatty + # alcohol that the ether lipids use, R holds the whole alkyl chain, carbinol + # carbon included. + "MAR10061": "fatty acyl-CoA pool (R without the carbonyl carbon) to fatty alcohol (R with the carbinol carbon)", +} + def _subsystems(rxn): """A reaction's subsystems as a set; the YAML gives either a list or a string.""" @@ -76,15 +97,20 @@ def _is_lumped(rxn): return rxn.id in LUMPED_REACTIONS or bool(_subsystems(rxn) & LUMPED_SUBSYSTEMS) -def _stale_lumped_entries(model, unbalanced_ids): - """Entries of LUMPED_REACTIONS the model no longer needs. +def _is_bridge(rxn): + """Whether the reaction joins two conventions of the placeholder elements.""" + return rxn.id in CONVENTION_BRIDGES + + +def _stale_lumped_entries(model, unbalanced_ids, entries=LUMPED_REACTIONS): + """Entries of LUMPED_REACTIONS, or of CONVENTION_BRIDGES, the model no longer needs. An identifier that is gone from the model, or whose reaction now balances in both mass and charge, no longer excludes anything and should be dropped from the list. """ stale = [] - for rid in sorted(LUMPED_REACTIONS): + for rid in sorted(entries): if rid not in model.reactions: stale.append(f"{rid} (not in the model)") elif rid not in unbalanced_ids: @@ -98,6 +124,7 @@ def main(): errored = [] unbalanced_ids = set() n_lumped = 0 + n_bridges = 0 for rxn in model.reactions: if rxn.boundary: continue @@ -109,7 +136,7 @@ def main(): # A reaction whose balance cannot be evaluated (usually a malformed # formula) is a finding, not something to hide: record it as its own # row so it shows up in the committed diff and the count. - if not _is_lumped(rxn): + if not (_is_lumped(rxn) or _is_bridge(rxn)): errored.append(rxn.id) rows.append((rxn.id, rxn.name or "", f"check_failed:{exc}", "")) continue @@ -119,6 +146,9 @@ def main(): if _is_lumped(rxn): n_lumped += 1 continue + if _is_bridge(rxn): + n_bridges += 1 + continue mass = {k: v for k, v in imbalance.items() if k != "charge"} charge = imbalance.get("charge", 0) rows.append(( @@ -137,15 +167,17 @@ def main(): print( f"Unbalanced reactions (excluding boundary, biomass and lumped): {len(rows)} " f"({n_mass} mass, {n_charge} charge, {len(errored)} could not be checked); " - f"{n_lumped} lumped pseudo-reaction(s) excluded" + f"{n_lumped} lumped pseudo-reaction(s) and {n_bridges} convention bridge(s) excluded" ) if errored: print(f"::warning::{len(errored)} reaction(s) could not be balance-checked: " f"{';'.join(errored[:20])}{' ...' if len(errored) > 20 else ''}") - stale = _stale_lumped_entries(model, unbalanced_ids) - if stale: - print(f"::warning::{len(stale)} entr(y/ies) of LUMPED_REACTIONS are no longer " - f"needed and can be dropped from code/test/balanceTest.py: {'; '.join(stale)}") + for name, entries in (("LUMPED_REACTIONS", LUMPED_REACTIONS), + ("CONVENTION_BRIDGES", CONVENTION_BRIDGES)): + stale = _stale_lumped_entries(model, unbalanced_ids, entries) + if stale: + print(f"::warning::{len(stale)} entr(y/ies) of {name} are no longer " + f"needed and can be dropped from code/test/balanceTest.py: {'; '.join(stale)}") if __name__ == "__main__": diff --git a/code/test/unit/test_balance_test.py b/code/test/unit/test_balance_test.py index b643f0d46..8894e9a74 100644 --- a/code/test/unit/test_balance_test.py +++ b/code/test/unit/test_balance_test.py @@ -79,3 +79,31 @@ def test_stale_entries_report_missing_and_balanced_reactions(): assert not any(line.startswith(kept) for line in stale) assert sum(1 for line in stale if "(not in the model)" in line) == \ len(balanceTest.LUMPED_REACTIONS) - 2 + + +def test_listed_bridges_are_skipped_whatever_their_subsystem(): + for rid in balanceTest.CONVENTION_BRIDGES: + assert balanceTest._is_bridge(_rxn(rid, {}, "Ether lipid metabolism")) + + +def test_an_unlisted_reaction_is_not_a_bridge(): + assert not balanceTest._is_bridge(_rxn("MAR09999", {}, "Ether lipid metabolism")) + + +def test_a_bridge_is_not_a_lumped_reaction(): + assert not set(balanceTest.CONVENTION_BRIDGES) & set(balanceTest.LUMPED_REACTIONS) + + +def test_every_bridge_reason_names_the_two_conventions(): + assert all(" to " in reason and len(reason) > 20 for reason in balanceTest.CONVENTION_BRIDGES.values()) + + +def test_stale_bridge_entries_use_the_given_list(): + model = cobra.Model("m") + kept, dropped = sorted(balanceTest.CONVENTION_BRIDGES)[:2] + model.add_reactions([_rxn(kept, {}), _rxn(dropped, {})]) + stale = balanceTest._stale_lumped_entries(model, {kept}, balanceTest.CONVENTION_BRIDGES) + assert f"{dropped} (balances)" in stale + assert not any(line.startswith(kept) for line in stale) + assert sum(1 for line in stale if "(not in the model)" in line) == \ + len(balanceTest.CONVENTION_BRIDGES) - 2 diff --git a/data/testResults/README.md b/data/testResults/README.md index e504cc937..3585cf862 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -73,6 +73,8 @@ Reactions whose elemental sums do not balance, from cobrapy's `check_mass_balanc `R` and `X` are treated as elements of their own rather than ignored, so a reaction using them is still expected to balance in them. Several do not, and that is a finding rather than noise. +Three reactions are excluded as convention bridges (`CONVENTION_BRIDGES` in `balanceTest.py`, each with its reason). They join two bookkeeping conventions of the placeholder elements, so the two sides do not count the same atoms: `MAR07197` and `MAR07282` take the residue from `[protein]`, where it is written out (`R2`), to `[protein]-L-serine` and `[protein]-L-asparagine`, where it sits inside `X`; `MAR10061` takes the fatty acyl-CoA pool, whose `R` starts after the carbonyl carbon, to the fatty alcohol, whose `R` holds the whole chain. Every run audits this list as it does the lumped reactions and warns about an entry the model no longer needs. + #### Charge-imbalanced reactions Reactions whose charge sums do not balance, with the same exclusions as above. From 10357a9304b7aba8934335bdc78c7c840bbfb057 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:08:44 +0100 Subject: [PATCH 16/44] doc: describe the table of the alkenyl ether lipid formulas #1153 --- data/modelCuration/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index 99013ccf9..429460383 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -49,3 +49,4 @@ Static dumps of external sources that were kept here during the Human1 series (S - `aflatoxinDialdehydeReductions.tsv`: per-entity table of the change "aflatoxin B1 dialdehyde reductions take NADPH" (`code/modelCuration/applyCurationTable.py`). - `dibenzoPyreneDiolEpoxide.tsv`: per-entity table of the change "formula of the dibenzo[a,l]pyrene diol epoxide and the proton of its formation" (`code/modelCuration/applyCurationTable.py`). - `nitricOxideSynthaseStoichiometry.tsv`: per-entity table of the change "stoichiometry of the arginine nitric oxide synthase reaction" (`code/modelCuration/applyCurationTable.py`). +- `alkenylEtherLipidFormulas.tsv`: per-entity table of the change "the vinyl ether carbons of the alkenyl ether lipids are counted inside R" (`code/modelCuration/applyCurationTable.py`). From b98bfed5c15e8b0c03dd1d21c2e55b0f006e2b65 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:42:02 +0100 Subject: [PATCH 17/44] fix: steroid Delta-isomerase of androstenedione has no cofactor HSD3B1 isomerises androst-5-ene-3,17-dione to androst-4-ene-3,17-dione without a cofactor (RHEA:43936). The two reactions added H+ and NAD+ => NADH, which left them short by two charges. Generated by `code/modelCuration/applyCurationTable.py --table data/modelCuration/steroidDeltaIsomerase.tsv`. #1153 --- data/modelCuration/steroidDeltaIsomerase.tsv | 3 +++ model/Human-GEM.yml | 6 ------ 2 files changed, 3 insertions(+), 6 deletions(-) create mode 100644 data/modelCuration/steroidDeltaIsomerase.tsv diff --git a/data/modelCuration/steroidDeltaIsomerase.tsv b/data/modelCuration/steroidDeltaIsomerase.tsv new file mode 100644 index 000000000..2e1b2d48f --- /dev/null +++ b/data/modelCuration/steroidDeltaIsomerase.tsv @@ -0,0 +1,3 @@ +entity field before after +MAR01970 metabolites MAM00971c:1.0;MAM01075c:-1.0;MAM02039c:-1.0;MAM02552c:-1.0;MAM02553c:1.0 MAM00971c:1.0;MAM01075c:-1.0 +MAR01971 metabolites MAM00971r:1.0;MAM01075r:-1.0;MAM02039r:-1.0;MAM02552r:-1.0;MAM02553r:1.0 MAM00971r:1.0;MAM01075r:-1.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 44f34c022..c9625c897 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -114355,9 +114355,6 @@ - metabolites: !!omap - MAM00971c: 1.0 - MAM01075c: -1.0 - - MAM02039c: -1.0 - - MAM02552c: -1.0 - - MAM02553c: 1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000203857 or ENSG00000203859 @@ -114375,9 +114372,6 @@ - metabolites: !!omap - MAM00971r: 1.0 - MAM01075r: -1.0 - - MAM02039r: -1.0 - - MAM02552r: -1.0 - - MAM02553r: 1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000203857 or ENSG00000203859 From 84fe6e1c2bfd30c656562f32e252afa619a40026 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:42:06 +0100 Subject: [PATCH 18/44] fix: the peroxidases oxidise two catechol estrogens per H2O2 A peroxidase oxidises two phenolic donors to two radicals with one H2O2 (RHEA:56136). The eight reactions wrote one donor with H+, which left them short by one charge. Generated by `code/modelCuration/applyCurationTable.py --table data/modelCuration/catecholEstrogenPeroxidase.tsv`. #1153 --- .../catecholEstrogenPeroxidase.tsv | 9 +++++ model/Human-GEM.yml | 40 ++++++++----------- 2 files changed, 25 insertions(+), 24 deletions(-) create mode 100644 data/modelCuration/catecholEstrogenPeroxidase.tsv diff --git a/data/modelCuration/catecholEstrogenPeroxidase.tsv b/data/modelCuration/catecholEstrogenPeroxidase.tsv new file mode 100644 index 000000000..7e35314f1 --- /dev/null +++ b/data/modelCuration/catecholEstrogenPeroxidase.tsv @@ -0,0 +1,9 @@ +entity field before after +MAR02061 metabolites MAM00650c:-1.0;MAM01792c:1.0;MAM02039c:-1.0;MAM02040c:2.0;MAM02041c:-1.0 MAM00650c:-2.0;MAM01792c:2.0;MAM02040c:2.0;MAM02041c:-1.0 +MAR02062 metabolites MAM00650l:-1.0;MAM01792l:1.0;MAM02039l:-1.0;MAM02040l:2.0;MAM02041l:-1.0 MAM00650l:-2.0;MAM01792l:2.0;MAM02040l:2.0;MAM02041l:-1.0 +MAR02063 metabolites MAM00650r:-1.0;MAM01792r:1.0;MAM02039r:-1.0;MAM02040r:2.0;MAM02041r:-1.0 MAM00650r:-2.0;MAM01792r:2.0;MAM02040r:2.0;MAM02041r:-1.0 +MAR02076 metabolites MAM01000c:-1.0;MAM01794c:1.0;MAM02039c:-1.0;MAM02040c:2.0;MAM02041c:-1.0 MAM01000c:-2.0;MAM01794c:2.0;MAM02040c:2.0;MAM02041c:-1.0 +MAR02077 metabolites MAM01000l:-1.0;MAM01794l:1.0;MAM02039l:-1.0;MAM02040l:2.0;MAM02041l:-1.0 MAM01000l:-2.0;MAM01794l:2.0;MAM02040l:2.0;MAM02041l:-1.0 +MAR02078 metabolites MAM01000r:-1.0;MAM01794r:1.0;MAM02039r:-1.0;MAM02040r:2.0;MAM02041r:-1.0 MAM01000r:-2.0;MAM01794r:2.0;MAM02040r:2.0;MAM02041r:-1.0 +MAR02099 metabolites MAM00411c:-1.0;MAM00649c:1.0;MAM02039c:1.0;MAM02040c:-2.0;MAM02041c:1.0 MAM00411c:-2.0;MAM00649c:2.0;MAM02040c:-2.0;MAM02041c:1.0 +MAR02100 metabolites MAM00411l:-1.0;MAM00649l:1.0;MAM02039l:1.0;MAM02040l:-2.0;MAM02041l:1.0 MAM00411l:-2.0;MAM00649l:2.0;MAM02040l:-2.0;MAM02041l:1.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index c9625c897..42780740b 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -116482,9 +116482,8 @@ - id: MAR02061 - name: peroxidase (2-hydroxyestrone) - metabolites: !!omap - - MAM00650c: -1.0 - - MAM01792c: 1.0 - - MAM02039c: -1.0 + - MAM00650c: -2.0 + - MAM01792c: 2.0 - MAM02040c: 2.0 - MAM02041c: -1.0 - lower_bound: -1000.0 @@ -116503,9 +116502,8 @@ - id: MAR02062 - name: peroxidase (2-hydroxyestrone) - metabolites: !!omap - - MAM00650l: -1.0 - - MAM01792l: 1.0 - - MAM02039l: -1.0 + - MAM00650l: -2.0 + - MAM01792l: 2.0 - MAM02040l: 2.0 - MAM02041l: -1.0 - lower_bound: -1000.0 @@ -116524,9 +116522,8 @@ - id: MAR02063 - name: peroxidase (2-hydroxyestrone) - metabolites: !!omap - - MAM00650r: -1.0 - - MAM01792r: 1.0 - - MAM02039r: -1.0 + - MAM00650r: -2.0 + - MAM01792r: 2.0 - MAM02040r: 2.0 - MAM02041r: -1.0 - lower_bound: -1000.0 @@ -116705,9 +116702,8 @@ - id: MAR02076 - name: peroxidase (4-hydroxyestrone) - metabolites: !!omap - - MAM01000c: -1.0 - - MAM01794c: 1.0 - - MAM02039c: -1.0 + - MAM01000c: -2.0 + - MAM01794c: 2.0 - MAM02040c: 2.0 - MAM02041c: -1.0 - lower_bound: -1000.0 @@ -116726,9 +116722,8 @@ - id: MAR02077 - name: peroxidase (4-hydroxyestrone) - metabolites: !!omap - - MAM01000l: -1.0 - - MAM01794l: 1.0 - - MAM02039l: -1.0 + - MAM01000l: -2.0 + - MAM01794l: 2.0 - MAM02040l: 2.0 - MAM02041l: -1.0 - lower_bound: -1000.0 @@ -116747,9 +116742,8 @@ - id: MAR02078 - name: peroxidase (4-hydroxyestrone) - metabolites: !!omap - - MAM01000r: -1.0 - - MAM01794r: 1.0 - - MAM02039r: -1.0 + - MAM01000r: -2.0 + - MAM01794r: 2.0 - MAM02040r: 2.0 - MAM02041r: -1.0 - lower_bound: -1000.0 @@ -116983,9 +116977,8 @@ - id: MAR02099 - name: peroxidase (17beta-estradiol-2,3-semiquinone) - metabolites: !!omap - - MAM00411c: -1.0 - - MAM00649c: 1.0 - - MAM02039c: 1.0 + - MAM00411c: -2.0 + - MAM00649c: 2.0 - MAM02040c: -2.0 - MAM02041c: 1.0 - lower_bound: -1000.0 @@ -117004,9 +116997,8 @@ - id: MAR02100 - name: peroxidase (17beta-estradiol-2,3-semiquinone) - metabolites: !!omap - - MAM00411l: -1.0 - - MAM00649l: 1.0 - - MAM02039l: 1.0 + - MAM00411l: -2.0 + - MAM00649l: 2.0 - MAM02040l: -2.0 - MAM02041l: 1.0 - lower_bound: -1000.0 From dea065a328d534f07a5b21ac4408d4c445c4cae4 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:42:11 +0100 Subject: [PATCH 19/44] fix: the oxidase of 4-cis-decenoyl-CoA reduces FAD The acyl-CoA oxidases pass their electrons to O2 (RHEA:38959), which this model writes as FAD => FADH2 and the reoxidation of FADH2 by MAR20114. The reaction released two protons instead. Generated by `code/modelCuration/applyCurationTable.py --table data/modelCuration/acylCoAOxidase4CisDecenoylCoA.tsv`. #1153 --- data/modelCuration/acylCoAOxidase4CisDecenoylCoA.tsv | 2 ++ model/Human-GEM.yml | 3 ++- 2 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 data/modelCuration/acylCoAOxidase4CisDecenoylCoA.tsv diff --git a/data/modelCuration/acylCoAOxidase4CisDecenoylCoA.tsv b/data/modelCuration/acylCoAOxidase4CisDecenoylCoA.tsv new file mode 100644 index 000000000..ff35fa2dd --- /dev/null +++ b/data/modelCuration/acylCoAOxidase4CisDecenoylCoA.tsv @@ -0,0 +1,2 @@ +entity field before after +MAR03321 metabolites MAM00980x:-1.0;MAM02039x:2.0;MAM03543x:1.0 MAM00980x:-1.0;MAM01802x:-1.0;MAM01803x:1.0;MAM03543x:1.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 42780740b..833139fd2 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -108278,7 +108278,8 @@ - name: acyl-CoA oxidase (4-cis-decenoyl-CoA) - metabolites: !!omap - MAM00980x: -1.0 - - MAM02039x: 2.0 + - MAM01802x: -1.0 + - MAM01803x: 1.0 - MAM03543x: 1.0 - lower_bound: 0.0 - upper_bound: 1000.0 From 6a0fe4435a3e399e48357e8dcfe72e6d55205268 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:42:15 +0100 Subject: [PATCH 20/44] fix: the lumped pristanoyl-CoA oxidation counts its three cycles The reaction releases two propanoyl-CoA and one acetyl-CoA, which takes three cycles with one FAD and one NAD+ reduced in each. It counted two FAD and five protons. Generated by `code/modelCuration/applyCurationTable.py --table data/modelCuration/pristanoylCoALumpedOxidation.tsv`. #1153 --- data/modelCuration/pristanoylCoALumpedOxidation.tsv | 2 ++ model/Human-GEM.yml | 6 +++--- 2 files changed, 5 insertions(+), 3 deletions(-) create mode 100644 data/modelCuration/pristanoylCoALumpedOxidation.tsv diff --git a/data/modelCuration/pristanoylCoALumpedOxidation.tsv b/data/modelCuration/pristanoylCoALumpedOxidation.tsv new file mode 100644 index 000000000..91687fdd8 --- /dev/null +++ b/data/modelCuration/pristanoylCoALumpedOxidation.tsv @@ -0,0 +1,2 @@ +entity field before after +MAR01600 metabolites MAM01261x:1.0;MAM01597x:-3.0;MAM01802x:-2.0;MAM01803x:2.0;MAM02039x:5.0;MAM02040x:-3.0;MAM02552x:-3.0;MAM02553x:3.0;MAM02774x:2.0;MAM03554x:1.0;MAM03887x:-1.0 MAM01261x:1.0;MAM01597x:-3.0;MAM01802x:-3.0;MAM01803x:3.0;MAM02039x:3.0;MAM02040x:-3.0;MAM02552x:-3.0;MAM02553x:3.0;MAM02774x:2.0;MAM03554x:1.0;MAM03887x:-1.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 833139fd2..2014d280a 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -201712,9 +201712,9 @@ - metabolites: !!omap - MAM01261x: 1.0 - MAM01597x: -3.0 - - MAM01802x: -2.0 - - MAM01803x: 2.0 - - MAM02039x: 5.0 + - MAM01802x: -3.0 + - MAM01803x: 3.0 + - MAM02039x: 3.0 - MAM02040x: -3.0 - MAM02552x: -3.0 - MAM02553x: 3.0 From 8d878df26a638c8efaaa0f6934ed0f7ff902a5d2 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:42:15 +0100 Subject: [PATCH 21/44] doc: describe the tables of the isomerase, peroxidase and oxidase stoichiometry #1153 --- data/modelCuration/README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index 429460383..788a8ff4a 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -50,3 +50,7 @@ Static dumps of external sources that were kept here during the Human1 series (S - `dibenzoPyreneDiolEpoxide.tsv`: per-entity table of the change "formula of the dibenzo[a,l]pyrene diol epoxide and the proton of its formation" (`code/modelCuration/applyCurationTable.py`). - `nitricOxideSynthaseStoichiometry.tsv`: per-entity table of the change "stoichiometry of the arginine nitric oxide synthase reaction" (`code/modelCuration/applyCurationTable.py`). - `alkenylEtherLipidFormulas.tsv`: per-entity table of the change "the vinyl ether carbons of the alkenyl ether lipids are counted inside R" (`code/modelCuration/applyCurationTable.py`). +- `steroidDeltaIsomerase.tsv`: per-entity table of the change "the Delta-isomerase of androstenedione has no cofactor" (`code/modelCuration/applyCurationTable.py`). +- `catecholEstrogenPeroxidase.tsv`: per-entity table of the change "the peroxidases oxidise two catechol estrogens per H2O2" (`code/modelCuration/applyCurationTable.py`). +- `acylCoAOxidase4CisDecenoylCoA.tsv`: per-entity table of the change "the oxidase of 4-cis-decenoyl-CoA reduces FAD" (`code/modelCuration/applyCurationTable.py`). +- `pristanoylCoALumpedOxidation.tsv`: per-entity table of the change "the lumped pristanoyl-CoA oxidation counts its three cycles" (`code/modelCuration/applyCurationTable.py`). From 81aa5e9debd0c4db40a1efaa96659a5fc0ebb5c7 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:51:21 +0100 Subject: [PATCH 22/44] fix: HSD3B acts on 5alpha-androstane-3beta,17beta-diol, not on androstenediol HSD3B1 interconverts 5alpha-dihydrotestosterone and 5alpha-androstane-3beta,17beta-diol (RHEA:42184, RHEA:16297). MAR02022, MAR02024 and MAR03400 wrote androstenediol, the Delta5 diol, which no other reaction uses, and were short by two charges. The new metabolite MAM20097 (ChEBI:18329) replaces MAM01336, which is deprecated, and the proton moves to the side where the reduction consumes it. The reactions follow data/modelCuration/androstanediolHsd3b.tsv (applyCurationTable.py); the metabolites were changed by hand. #1153 --- .../deprecatedMetabolites.tsv | 3 ++ data/modelCuration/README.md | 1 + data/modelCuration/androstanediolHsd3b.tsv | 4 +++ model/Human-GEM.yml | 36 +++++++++---------- model/metabolites.tsv | 6 ++-- 5 files changed, 29 insertions(+), 21 deletions(-) create mode 100644 data/modelCuration/androstanediolHsd3b.tsv diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 27be3f2fe..1d234656b 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2451,3 +2451,6 @@ MAM01036c MAM01036 C04487 CHEBI:8439 M01036 MNXM78106 *NC(=O)[C@H](CC[C@H] MAM00232c MAM00232 C04759 M00232 MNXM91041 *NC(=O)[C@H](CC[C@H](CN)O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)NC(*)=O cpd12607 m00232c m00232c MAM01778g MAM01778 elaid C01712 HMDB0000573 CHEBI:30825 5461071 LMFA01030073 MNXM1364394 CCCCCCCC/C=C/CCCCCCCC(=O)[O-] InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/p-1/b10-9+ cpd01179 MAM01267c MAM01267 HC02116 HC02116 HC02116 MNXM166880 m01267c m01267c +MAM01336c MAM01336 C04295 C04295 HMDB0003818 CHEBI:2710 10634 LMST02020005 C04295 MNXM733638 C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-17,20-21H,4-11H2,1-2H3/t13-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02637 m01336c m01336c +MAM01336r MAM01336 C04295 C04295 HMDB0003818 CHEBI:2710 10634 LMST02020005 C04295 MNXM733638 C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-17,20-21H,4-11H2,1-2H3/t13-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02637 m01336r m01336r +MAM01336m MAM01336 C04295 C04295 HMDB0003818 CHEBI:2710 10634 LMST02020005 C04295 MNXM733638 C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-17,20-21H,4-11H2,1-2H3/t13-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02637 m01336m diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index 788a8ff4a..e132e22ec 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -54,3 +54,4 @@ Static dumps of external sources that were kept here during the Human1 series (S - `catecholEstrogenPeroxidase.tsv`: per-entity table of the change "the peroxidases oxidise two catechol estrogens per H2O2" (`code/modelCuration/applyCurationTable.py`). - `acylCoAOxidase4CisDecenoylCoA.tsv`: per-entity table of the change "the oxidase of 4-cis-decenoyl-CoA reduces FAD" (`code/modelCuration/applyCurationTable.py`). - `pristanoylCoALumpedOxidation.tsv`: per-entity table of the change "the lumped pristanoyl-CoA oxidation counts its three cycles" (`code/modelCuration/applyCurationTable.py`). +- `androstanediolHsd3b.tsv`: per-entity table of the reaction part of the change "3beta-hydroxysteroid dehydrogenase acts on 5alpha-androstane-3beta,17beta-diol" (`code/modelCuration/applyCurationTable.py`); the metabolite part was made by hand. diff --git a/data/modelCuration/androstanediolHsd3b.tsv b/data/modelCuration/androstanediolHsd3b.tsv new file mode 100644 index 000000000..d3500160f --- /dev/null +++ b/data/modelCuration/androstanediolHsd3b.tsv @@ -0,0 +1,4 @@ +entity field before after +MAR02022 metabolites MAM01069c:-1.0;MAM01336c:1.0;MAM02039c:1.0;MAM02552c:1.0;MAM02553c:-1.0 MAM01069c:-1.0;MAM02039c:-1.0;MAM02552c:1.0;MAM02553c:-1.0;MAM20097c:1.0 +MAR02024 metabolites MAM01069r:-1.0;MAM01336r:1.0;MAM02039r:1.0;MAM02552r:1.0;MAM02553r:-1.0 MAM01069r:-1.0;MAM02039r:-1.0;MAM02552r:1.0;MAM02553r:-1.0;MAM20097r:1.0 +MAR03400 metabolites MAM01069m:1.0;MAM01336m:-1.0;MAM02039m:-1.0;MAM02552m:-1.0;MAM02553m:1.0 MAM01069m:1.0;MAM02039m:1.0;MAM02552m:-1.0;MAM02553m:1.0;MAM20097m:-1.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 2014d280a..1d7af8d7d 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -14623,19 +14623,19 @@ - formula: C22H37NO2 - metFrom: HMRdatabase - !!omap - - id: MAM01336c - - name: androstenediol + - id: MAM20097c + - name: 5alpha-androstane-3beta,17beta-diol - compartment: c - charge: 0.0 - - formula: C19H30O2 - - metFrom: HMRdatabase + - formula: C19H32O2 + - metFrom: HumanGEM - !!omap - - id: MAM01336r - - name: androstenediol + - id: MAM20097r + - name: 5alpha-androstane-3beta,17beta-diol - compartment: r - charge: 0.0 - - formula: C19H30O2 - - metFrom: HMRdatabase + - formula: C19H32O2 + - metFrom: HumanGEM - !!omap - id: MAM01337c - name: androsterone sulfate @@ -41615,12 +41615,12 @@ - formula: C19H30O2 - metFrom: Recon3D - !!omap - - id: MAM01336m - - name: androstenediol + - id: MAM20097m + - name: 5alpha-androstane-3beta,17beta-diol - compartment: m - charge: 0.0 - - formula: C19H30O2 - - metFrom: Recon3D + - formula: C19H32O2 + - metFrom: HumanGEM - !!omap - id: MAM00708r - name: 3(S)-hydroxy-all-cis-8,11,14,17-eicosatetraenoyl-CoA @@ -114671,10 +114671,10 @@ - name: 3beta-hydroxy-Delta(5)-steroid dehydrogenase (5-alpha-dihydrotestosterone) - metabolites: !!omap - MAM01069c: -1.0 - - MAM01336c: 1.0 - - MAM02039c: 1.0 + - MAM02039c: -1.0 - MAM02552c: 1.0 - MAM02553c: -1.0 + - MAM20097c: 1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000203857 or ENSG00000203859 @@ -114691,10 +114691,10 @@ - name: 3beta-hydroxy-Delta(5)-steroid dehydrogenase (5-alpha-dihydrotestosterone) - metabolites: !!omap - MAM01069r: -1.0 - - MAM01336r: 1.0 - - MAM02039r: 1.0 + - MAM02039r: -1.0 - MAM02552r: 1.0 - MAM02553r: -1.0 + - MAM20097r: 1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000203857 or ENSG00000203859 @@ -208952,10 +208952,10 @@ - name: 3Beta-Hydroxy-Delta5-Steroid Dehydrogenase - metabolites: !!omap - MAM01069m: 1.0 - - MAM01336m: -1.0 - - MAM02039m: -1.0 + - MAM02039m: 1.0 - MAM02552m: -1.0 - MAM02553m: 1.0 + - MAM20097m: -1.0 - lower_bound: -1000.0 - upper_bound: 1000.0 - gene_reaction_rule: ENSG00000203857 or ENSG00000203859 diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 143fc4b5e..97f96f91e 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -2083,8 +2083,8 @@ MAM01334x MAM01334 amp C00020 HMDB0000045 CHEBI:16027 6083 HC00030 amp MNXM728 MAM01334r MAM01334 amp C00020 HMDB0000045 CHEBI:16027 6083 HC00030 amp MNXM728294 Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]1O InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/p-2/t4-,6-,7-,10-/m1/s1 cpd00018 m01334r m01334r MAM01334e MAM01334 amp C00020 HMDB0000045 CHEBI:16027 6083 HC00030 amp MNXM728294 Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]1O InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/p-2/t4-,6-,7-,10-/m1/s1 cpd00018 m01334s m01334s MAM01335c MAM01335 C11695 C11695 HMDB0004080 CHEBI:2700 5281969 LMFA08040001 C11695 MNXM737355 CCCCC/C=C\C/C=C\C/C=C\C/C=C\CCCC(=O)NCCO InChI=1S/C22H37NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-22(25)23-20-21-24/h6-7,9-10,12-13,15-16,24H,2-5,8,11,14,17-21H2,1H3,(H,23,25)/b7-6-,10-9-,13-12-,16-15- cpd08505 m01335c m01335c -MAM01336c MAM01336 C04295 C04295 HMDB0003818 CHEBI:2710 10634 LMST02020005 C04295 MNXM733638 C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-17,20-21H,4-11H2,1-2H3/t13-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02637 m01336c m01336c -MAM01336r MAM01336 C04295 C04295 HMDB0003818 CHEBI:2710 10634 LMST02020005 C04295 MNXM733638 C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-17,20-21H,4-11H2,1-2H3/t13-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02637 m01336r m01336r +MAM20097c MAM20097 C12525 HMDB0000493 CHEBI:18329 LMST02020053 C[C@]12CC[C@H](O)C[C@@H]1CC[C@@H]1[C@@H]2CC[C@]2(C)[C@@H](O)CC[C@@H]12 InChI=1S/C19H32O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h12-17,20-21H,3-11H2,1-2H3/t12-,13-,14-,15-,16-,17-,18-,19-/m0/s1 +MAM20097r MAM20097 C12525 HMDB0000493 CHEBI:18329 LMST02020053 C[C@]12CC[C@H](O)C[C@@H]1CC[C@@H]1[C@@H]2CC[C@]2(C)[C@@H](O)CC[C@@H]12 InChI=1S/C19H32O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h12-17,20-21H,3-11H2,1-2H3/t12-,13-,14-,15-,16-,17-,18-,19-/m0/s1 MAM01337c MAM01337 CE6031 HMDB0002759 CHEBI:133003 159663 LMST05020001 CE6031 CE6031 MNXM42074 C[C@]12CC[C@@H](OS(=O)(=O)[O-])C[C@@H]1CC[C@@H]1[C@@H]2CC[C@]2(C)C(=O)CC[C@@H]12 InChI=1S/C19H30O5S/c1-18-9-7-13(24-25(21,22)23)11-12(18)3-4-14-15-5-6-17(20)19(15,2)10-8-16(14)18/h12-16H,3-11H2,1-2H3,(H,21,22,23)/p-1/t12-,13+,14-,15-,16-,18-,19-/m0/s1 m01337c m01337c MAM01338c MAM01338 andrstrn C00523 HMDB0000031 CHEBI:16032 12306765 LMST02020001 andrstrn MNXM730462 C[C@]12CC[C@H]3[C@@H](CC[C@H]4C[C@H](O)CC[C@@]43C)[C@@H]1CCC2=O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h12-16,20H,3-11H2,1-2H3/t12-,13+,14-,15-,16-,18-,19-/m0/s1 cpd00409 m01338c m01338c MAM01338r MAM01338 andrstrn C00523 HMDB0000031 CHEBI:16032 12306765 LMST02020001 andrstrn MNXM730462 C[C@]12CC[C@H]3[C@@H](CC[C@H]4C[C@H](O)CC[C@@]43C)[C@@H]1CCC2=O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h12-16,20H,3-11H2,1-2H3/t12-,13+,14-,15-,16-,18-,19-/m0/s1 cpd00409 m01338r m01338r @@ -5939,7 +5939,7 @@ MAM03029r MAM03029 CE5114 CHEBI:76412 72193768 CE5114 CE5114 MNXM165187 CCCC MAM01769r MAM01769 CE4812 CE4812 CE4812 MNXM145823 CC/C=C\C/C=C\C/C=C\C/C=C\CCCC/C=C/C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)([O-])[O-] InChI=1S/C41H64N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-32(50)69-25-24-43-31(49)22-23-44-39(53)36(52)41(2,3)27-62-68(59,60)65-67(57,58)61-26-30-35(64-66(54,55)56)34(51)40(63-30)48-29-47-33-37(42)45-28-46-38(33)48/h5-6,8-9,11-12,14-15,20-21,28-30,34-36,40,51-52H,4,7,10,13,16-19,22-27H2,1-3H3,(H,43,49)(H,44,53)(H,57,58)(H,59,60)(H2,42,45,46)(H2,54,55,56)/p-4/b6-5-,9-8-,12-11-,15-14-,21-20+/t30-,34-,35-,36+,40-/m1/s1 m01769r MAM00811r MAM00811 CE4811 CE4811 MNXM164249 CC/C=C\C/C=C\C/C=C\C/C=C\CCCCC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)([O-])[O-] InChI=1S/C41H64N7O18P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-29(49)24-32(51)70-23-22-43-31(50)20-21-44-39(54)36(53)41(2,3)26-63-69(60,61)66-68(58,59)62-25-30-35(65-67(55,56)57)34(52)40(64-30)48-28-47-33-37(42)45-27-46-38(33)48/h5-6,8-9,11-12,14-15,27-28,30,34-36,40,52-53H,4,7,10,13,16-26H2,1-3H3,(H,43,50)(H,44,54)(H,58,59)(H,60,61)(H2,42,45,46)(H2,55,56,57)/p-4/b6-5-,9-8-,12-11-,15-14-/t30-,34-,35-,36+,40-/m1/s1 cpd35847 m00811r MAM01069m MAM01069 5adtststerone C03917 HMDB0002961 CHEBI:16330 10635 LMST02020042 5adtststerone MNXM730284 C[C@]12CC[C@H]3[C@@H](CC[C@H]4CC(=O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h12,14-17,21H,3-11H2,1-2H3/t12-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02435 m01069m -MAM01336m MAM01336 C04295 C04295 HMDB0003818 CHEBI:2710 10634 LMST02020005 C04295 MNXM733638 C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-17,20-21H,4-11H2,1-2H3/t13-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02637 m01336m +MAM20097m MAM20097 C12525 HMDB0000493 CHEBI:18329 LMST02020053 C[C@]12CC[C@H](O)C[C@@H]1CC[C@@H]1[C@@H]2CC[C@]2(C)[C@@H](O)CC[C@@H]12 InChI=1S/C19H32O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h12-17,20-21H,3-11H2,1-2H3/t12-,13-,14-,15-,16-,17-,18-,19-/m0/s1 MAM00708r MAM00708 CE4810 CHEBI:195630 91819744 CE4810 CE4810 MNXM739579 CC/C=C\C/C=C\C/C=C\C/C=C\CCCCC(O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)([O-])[O-] InChI=1S/C41H66N7O18P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-29(49)24-32(51)70-23-22-43-31(50)20-21-44-39(54)36(53)41(2,3)26-63-69(60,61)66-68(58,59)62-25-30-35(65-67(55,56)57)34(52)40(64-30)48-28-47-33-37(42)45-27-46-38(33)48/h5-6,8-9,11-12,14-15,27-30,34-36,40,49,52-53H,4,7,10,13,16-26H2,1-3H3,(H,43,50)(H,44,54)(H,58,59)(H,60,61)(H2,42,45,46)(H2,55,56,57)/p-4/b6-5-,9-8-,12-11-,15-14-/t29?,30-,34-,35-,36+,40-/m1/s1 m00708r MAM00679r MAM00679 CE4821 CE4821 MNXM730934 CC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CCC/C=C/C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)([O-])[O-] InChI=1S/C43H66N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-34(52)71-27-26-45-33(51)24-25-46-41(55)38(54)43(2,3)29-64-70(61,62)67-69(59,60)63-28-32-37(66-68(56,57)58)36(53)42(65-32)50-31-49-35-39(44)47-30-48-40(35)50/h5-6,8-9,11-12,14-15,17-18,22-23,30-32,36-38,42,53-54H,4,7,10,13,16,19-21,24-29H2,1-3H3,(H,45,51)(H,46,55)(H,59,60)(H,61,62)(H2,44,47,48)(H2,56,57,58)/p-4/b6-5-,9-8-,12-11-,15-14-,18-17-,23-22+/t32-,36-,37-,38+,42-/m1/s1 m00679r MAM00863r MAM00863 CE4819 CE4819 MNXM730960 CC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CCCC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1OP(=O)([O-])[O-] InChI=1S/C43H66N7O18P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-31(51)26-34(53)72-25-24-45-33(52)22-23-46-41(56)38(55)43(2,3)28-65-71(62,63)68-70(60,61)64-27-32-37(67-69(57,58)59)36(54)42(66-32)50-30-49-35-39(44)47-29-48-40(35)50/h5-6,8-9,11-12,14-15,17-18,29-30,32,36-38,42,54-55H,4,7,10,13,16,19-28H2,1-3H3,(H,45,52)(H,46,56)(H,60,61)(H,62,63)(H2,44,47,48)(H2,57,58,59)/p-4/b6-5-,9-8-,12-11-,15-14-,18-17-/t32-,36-,37-,38+,42-/m1/s1 m00863r From 08ec3df77c14bca05aded8a07ab87467b5983ee4 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 11:56:25 +0100 Subject: [PATCH 23/44] fix: remove MAR02313, the duplicate of the stearidonic acid ligase that makes stearoyl-CoA MAR02313 came from Recon3D (BiGG r1253), where the activation of stearidonic acid in the endoplasmic reticulum is written with stearoyl-CoA as the product and eight protons as hydrogens. MAR02982 is the same ligase with the correct product, (6Z,9Z,12Z,15Z)-octadecatetraenoyl-CoA, and carries all genes of MAR02313 (and ACSBG1), the same EC number and the same bounds. MAR02982 now also holds the reference PMID:8584017 and the source Recon3D of the removed reaction. The cross-references of r1253 describe the saturated product and stay in the deprecated list. The reference and the source follow data/modelCuration/stearidonicAcidLigaseDuplicate.tsv (applyCurationTable.py); the removal was made by hand. #1153 --- .../deprecatedReactions.tsv | 1 + data/modelCuration/README.md | 1 + .../stearidonicAcidLigaseDuplicate.tsv | 3 +++ model/Human-GEM.yml | 25 ++----------------- model/reactions.tsv | 1 - 5 files changed, 7 insertions(+), 24 deletions(-) create mode 100644 data/modelCuration/stearidonicAcidLigaseDuplicate.tsv diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 569b37cb5..e9401ee97 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -638,3 +638,4 @@ MAR08227 GAO2 GAO2 MNXR100038 HMR_8227 RCR10831 0 HMR_8227 MAR05381 R02021 RE3009C RE3009C rxn05239 HMR_5381 RCR10548 0 RHEA:11724 HMR_5381 MAR04188 r1332 r1332 MNXR105460 HMR_4188 RCR14479 0 HMR_4188 MAR01506 LRAT1 LRAT1 MNXR101236 0 LRAT1 +MAR02313 r1253 r1253 MNXR163357 0 r1253 diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index e132e22ec..62f2365fe 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -55,3 +55,4 @@ Static dumps of external sources that were kept here during the Human1 series (S - `acylCoAOxidase4CisDecenoylCoA.tsv`: per-entity table of the change "the oxidase of 4-cis-decenoyl-CoA reduces FAD" (`code/modelCuration/applyCurationTable.py`). - `pristanoylCoALumpedOxidation.tsv`: per-entity table of the change "the lumped pristanoyl-CoA oxidation counts its three cycles" (`code/modelCuration/applyCurationTable.py`). - `androstanediolHsd3b.tsv`: per-entity table of the reaction part of the change "3beta-hydroxysteroid dehydrogenase acts on 5alpha-androstane-3beta,17beta-diol" (`code/modelCuration/applyCurationTable.py`); the metabolite part was made by hand. +- `stearidonicAcidLigaseDuplicate.tsv`: per-entity table of the change "MAR02982 keeps the reference and the source of its removed duplicate MAR02313" (`code/modelCuration/applyCurationTable.py`); the removal itself was made by hand. diff --git a/data/modelCuration/stearidonicAcidLigaseDuplicate.tsv b/data/modelCuration/stearidonicAcidLigaseDuplicate.tsv new file mode 100644 index 000000000..a57e8e34f --- /dev/null +++ b/data/modelCuration/stearidonicAcidLigaseDuplicate.tsv @@ -0,0 +1,3 @@ +entity field before after +MAR02982 references PMID:8584017 +MAR02982 rxnFrom HMRdatabase HMRdatabase;Recon3D diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 1d7af8d7d..e8d63faaa 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -86935,7 +86935,8 @@ - annotation: !!omap - ec-code: - 6.2.1.3 - - rxnFrom: HMRdatabase + - references: PMID:8584017 + - rxnFrom: HMRdatabase;Recon3D - confidence_score: 0.0 - !!omap - id: MAR02983 @@ -204334,28 +204335,6 @@ - references: PMID:8584017 - rxnFrom: Recon3D - confidence_score: 0.0 - - !!omap - - id: MAR02313 - - name: long-chain-fatty-acid-CoA ligase (stearidonic acid to stearoyl-CoA) - - metabolites: !!omap - - MAM01334r: 1.0 - - MAM01371r: -1.0 - - MAM01597r: -1.0 - - MAM02039r: -8.0 - - MAM02759r: 1.0 - - MAM02939r: -1.0 - - MAM02941r: 1.0 - - lower_bound: 0.0 - - upper_bound: 1000.0 - - gene_reaction_rule: ENSG00000068366 or ENSG00000123983 or ENSG00000130377 or ENSG00000140284 or ENSG00000151726 or ENSG00000164398 or ENSG00000197142 - - subsystem: - - Fatty acid oxidation - - annotation: !!omap - - ec-code: - - 6.2.1.3 - - references: PMID:8584017 - - rxnFrom: Recon3D - - confidence_score: 0.0 - !!omap - id: MAR02316 - name: Vesicular Transport diff --git a/model/reactions.tsv b/model/reactions.tsv index 274e6eb68..476ec349b 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -8323,7 +8323,6 @@ MAR02306 r1165 r1165 MNXR105439 0 r1165 MAR02308 r1186 0 r1186 MAR02310 r1251 r1251 MNXR105452 0 r1251 MAR02312 r1252 r1252 MNXR105452 0 r1252 -MAR02313 r1253 r1253 MNXR163357 0 r1253 MAR02316 r1298 r1298 MNXR101114 0 r1298 MAR02318 r1301 r1301 MNXR192006 rxn28606 0 RHEA:33655 r1301 MAR02320 r1303 r1303 MNXR99102 0 r1303 From 97740b1e5cd042e4611fa8c1b63b676be65e25b5 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 12:59:45 +0100 Subject: [PATCH 24/44] doc: registry rows for the papers on the retinol and NNK reactions Leo 1989 (CYP2C8 and retinol), Martras 2004 (ADH on ring-oxidized retinoids) and the Hecht 1998 review (keto acid and hydroxy acid of NNK), read in full. #1153 --- literature/registry.md | 3 +++ literature/registry.tsv | 3 +++ 2 files changed, 6 insertions(+) diff --git a/literature/registry.md b/literature/registry.md index c7cd94715..f9d13c22b 100644 --- a/literature/registry.md +++ b/literature/registry.md @@ -83,6 +83,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Hallam TJ et al. (1984). The role of cytoplasmic free calcium in the responses of quin2-loaded human platelets to vasopressin. *Biochemical Journal*. [doi:10.1042/bj2210897](https://doi.org/10.1042/bj2210897) | Homo sapiens | | `MAR11311` | Quin2-loaded human platelets had a basal cytosolic free Ca2+ of about 100 nM (127 +/- 10 nM) and vasopressin raised it to about 700 nM in 1 mM external Ca2+, mainly by influx across the plasma membrane. The 1 mM figure is the medium concentration, not a measured in vivo gradient; the direction of net influx is inferred. | Abstract; Results p.2 | metabolite measurement | full text | Human-GEM#1173 | | Hart T et al. (2015). High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. *Cell*. [doi:10.1016/j.cell.2015.11.015](https://doi.org/10.1016/j.cell.2015.11.015), [PMID:26627737](https://pubmed.ncbi.nlm.nih.gov/26627737/) | Homo sapiens | genome-wide | | CRISPR fitness screens in five human cell lines (DLD1, GBM, HCT116, HeLa, RPE1); the reference for Human-GEM's gene-essentiality test. | Abstract | genetic screen | abstract | , doc/nefa-pool.md | | Hata K et al. (2002). Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. *Development*. [doi:10.1242/dev.129.8.1983](https://doi.org/10.1242/dev.129.8.1983), [PMID:11934864](https://pubmed.ncbi.nlm.nih.gov/11934864/) | Mus musculus | Dnmt3l | | Dnmt3L, a Dnmt3a and Dnmt3b homolog without methyltransferase activity, is required in mice for establishing maternal methylation imprints and for correct expression of maternally imprinted genes; it interacts with Dnmt3a and Dnmt3b and co-localizes with them in transfected cell nuclei, and Dnmt3a-/- Dnmt3b+/- mice show the same failure of maternal imprinting. Dnmt3a and Dnmt3L are also required for spermatogenesis. | Abstract | knockout phenotype, localization | abstract | Human-GEM#1155 | +| Hecht SS (1998). Biochemistry, Biology, and Carcinogenicity of Tobacco-Specific N-Nitrosamines. *Chemical Research in Toxicology*. [doi:10.1021/tx980005y](https://doi.org/10.1021/tx980005y), [PMID:9625726](https://pubmed.ncbi.nlm.nih.gov/9625726/) | multiple | | `MAR07070`, `MAR07076` | Review of the metabolism of the tobacco-specific nitrosamines. It states that keto acid is formed in vivo from keto alcohol (HPB) in rats and in some in vitro systems (cultured rat oral tissue and esophagus), that keto acid is also a likely oxidation product of keto aldehyde although this does not seem to have been investigated, and that hydroxy acid arises from NNAL by further oxidation of the lactol and the diol and not by reduction of keto acid. It names no enzyme or cofactor for these oxidations. Limits: a review that cites the underlying studies; the rat data are cited from other work | Sections 2.1.1.4 (alpha-methyl hydroxylation) and 2.1.3.3 (alpha-hydroxylation) | review | full text | Human-GEM#1153 | | Heikkinen J et al. (2000). Lysyl Hydroxylase 3 Is a Multifunctional Protein Possessing Collagen Glucosyltransferase Activity. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m006203200](https://doi.org/10.1074/jbc.m006203200) | Homo sapiens | PLOD3 | `MAR06984`, `MAR06985` | Human lysyl hydroxylase isoform 3 has both lysyl hydroxylase and collagen glucosyltransferase activity, while LH1 and LH2 lack the glucosyltransferase activity; antibodies partly inhibited the activity in fibroblast extracts and mutagenesis separated the two active sites. Galactosyltransferase activity was not tested, so it supports the glucosylation step (MAR06985) but not the galactosylation (MAR06984). | Abstract | enzyme assay | abstract | Human-GEM#1174 | | Hermann A et al. (2003). The Human Dnmt2 Has Residual DNA-(Cytosine-C5) Methyltransferase Activity. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m305448200](https://doi.org/10.1074/jbc.m305448200), [PMID:12794065](https://pubmed.ncbi.nlm.nih.gov/12794065/) | Homo sapiens | DNMT2, TRDMT1 | `MAR08641` | Purified human DNMT2 showed weak DNA methyltransferase activity in two independent in vitro assays, with methylation at CG sites in a loose ttnCGga(g/a) consensus. | Abstract | enzyme assay | abstract | Human-GEM#1155 | | Herraiz T (2003). L-tryptophan reacts with naturally occurring and food-occurring phenolic aldehydes to give phenolic tetrahydro-beta-carboline alkaloids: activity as antioxidants and free radical scavengers. *Journal of Agricultural and Food Chemistry*. [doi:10.1021/jf0210066](https://doi.org/10.1021/jf0210066) | in vitro (chemistry) | | | Benzaldehyde and several phenolic aldehydes condensed with L-tryptophan in aqueous acid (heat needed for all but benzaldehyde) to give tetrahydro-beta-carboline-3-carboxylic acids as cis and trans isomers. The study shows aldehyde condensation only: the product is the tetrahydro acid, not the aromatic beta-carboline, and tryptophan without an aldehyde was not tested. | Abstract | metabolite measurement | full text | Human-GEM#1173, Human-GEM#1133 | @@ -114,6 +115,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Leal NA et al. (2004). Human ATP:Cob(I)alamin Adenosyltransferase and Its Interaction with Methionine Synthase Reductase. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m405449200](https://doi.org/10.1074/jbc.m405449200), [PMID:15347655](https://pubmed.ncbi.nlm.nih.gov/15347655/) | Homo sapiens | MTRR, MMAB | `MAR08615` | Purified recombinant human MMAB (ATP:cob(I)alamin adenosyltransferase) variants 239K and 239M had specific activities of 220 and 190 nmol per min per mg, with Km values of 6.3 and 6.9 micromolar for ATP and 1.2 and 1.6 micromolar for cob(I)alamin. In a reconstituted in vitro system, purified human methionine synthase reductase reduced cob(II)alamin to cob(I)alamin, which MMAB adenosylated to AdoCbl, with an optimum of about 4 MSR per ATR and evidence that the two proteins interact so the cob(I)alamin intermediate is sequestered. | Abstract | enzyme assay | abstract | Human-GEM#1152 | | Lehn DA, Brown LJ (1994). The sequence of a human mitochondrial glycerol-3-phosphate dehydrogenase-encoding cDNA. *Gene*. [doi:10.1016/0378-1119(94)90469-3](https://doi.org/10.1016/0378-1119(94)90469-3) | Homo sapiens | GPD2 | `MAR00483` | Reports the cDNA sequence from a HeLa library for human mitochondrial glycerol-3-phosphate dehydrogenase (727 amino acids, 96% similar to the rat protein), with calmodulin-like Ca2+-binding sites and FAD- and putative glycerol-phosphate-binding sites. It is a sequence paper: the human enzyme, not E. coli GlpD, so it fits MAR00449 but is not evidence for the E. coli reference on MAR00483 (as cited in v2.0.1). | Abstract | genome analysis | abstract | Human-GEM#1172 | | Lemonde HA et al. (2003). Mutations in SRD5B1 (AKR1D1), the gene encoding delta(4)-3-oxosteroid 5beta-reductase, in hepatitis and liver failure in infancy. *Gut*. [doi:10.1136/gut.52.10.1494](https://doi.org/10.1136/gut.52.10.1494), [PMID:12970144](https://pubmed.ncbi.nlm.nih.gov/12970144/) | Homo sapiens | AKR1D1 | | Three infants with neonatal cholestatic liver disease whose main urinary and plasma bile acids were 3-oxo-delta4 species carried homozygous AKR1D1 (SRD5B1) mutations (two missense, one frameshift). Three patients; it describes the accumulating bile acids and not the order of steps in side-chain shortening. | Abstract | clinical, genome analysis | abstract | Human-GEM#1133, Human-GEM#1174 | +| Leo MA et al. (1989). Metabolism of retinol and retinoic acid by human liver cytochrome P450IIC8. *Archives of Biochemistry and Biophysics*. [doi:10.1016/0003-9861(89)90112-4](https://doi.org/10.1016/0003-9861(89)90112-4), [PMID:2916844](https://pubmed.ncbi.nlm.nih.gov/2916844/) | Homo sapiens | CYP2C8 | `MAR06634` | Human liver microsomes from nine subjects, and a reconstituted system with purified CYP2C8, NADPH and P450 reductase, converted retinol to 4-hydroxyretinol and other polar metabolites that were not identified (Km 0.071 mM, Vmax 1.73 nmol per min per nmol P450); purified CYP2C9 and CYP2E1 had no significant retinol hydroxylase activity, and an antibody against CYP2C8 inhibited the reaction in microsomes. The CYP2C8 system also converted retinoic acid to polar products that include 4-hydroxy- and 4-oxoretinoic acid. 4-Oxoretinol is not reported as a product of retinol. Limits: in vitro; the other polar products were not identified; CYP26A1 was not tested | Abstract; Results (Table I, Fig. 1); the retinoic acid paragraph of the Results | enzyme assay | full text | Human-GEM#1153 | | Leonard AE et al. (2000). Cloning of a human cDNA encoding a novel enzyme involved in the elongation of long-chain polyunsaturated fatty acids. *Biochemical Journal*. [doi:10.1042/bj3500765](https://doi.org/10.1042/bj3500765), [PMID:10970790](https://pubmed.ncbi.nlm.nih.gov/10970790/) | Homo sapiens | ELOVL5 | | A human liver cDNA, HELO1 (ELOVL5), encoding a 299-residue protein with a histidine-rich domain, elongated polyunsaturated fatty acids when expressed in Saccharomyces cerevisiae: 18:3n-6 to 20:3n-6, 20:4n-6 to 22:4n-6, 18:4n-3 to 20:4n-3, 20:5n-3 to 22:5n-3 and 18:3n-3 to 20:3n-3, with highest mRNA in adrenal gland and testis. No reduction or retroconversion of docosahexaenoic acid is reported. | Abstract | expression, enzyme assay | abstract | Human-GEM#1151 | | Leonard AE et al. (2002). Identification and expression of mammalian long‐chain PUFA elongation enzymes. *Lipids*. [doi:10.1007/s11745-002-0955-6](https://doi.org/10.1007/s11745-002-0955-6), [PMID:12371743](https://pubmed.ncbi.nlm.nih.gov/12371743/) | Homo sapiens; Mus musculus | ELOVL2, Elovl2 | `MAR03415`, `MAR03440` | Human ELOVL2 (296 residues) and mouse Elovl2 (292 residues) expressed in Saccharomyces cerevisiae elongated C20 and C22 PUFA, converting 20:4n-6 to 22:4n-6, 22:4n-6 to 24:4n-6, 20:5n-3 to 22:5n-3 and 22:5n-3 to 24:5n-3; mouse Elovl2 expressed in mouse L cells incubated with C20 and C22 substrates raised 24:4n-6 and 24:5n-3 levels. | Abstract | enzyme assay, expression | abstract | Human-GEM#1151 | | Leśniak RK et al. (2017). Human carnitine biosynthesis proceeds via (2S,3S)-3-hydroxy-Nε-trimethyllysine. *Chemical Communications*. [doi:10.1039/c6cc08381a](https://doi.org/10.1039/c6cc08381a) | Homo sapiens | TMLHE | `MAR06979` | Enzymatic and asymmetric chemical synthesis experiments define the product of trimethyllysine hydroxylase (TMLH, the first step of mammalian carnitine biosynthesis) as the (2S,3S) stereoisomer of 3-hydroxy-N-epsilon-trimethyllysine; the abstract does not report kinetics or a cell-based test. | Abstract | enzyme assay | abstract | Human-GEM | @@ -134,6 +136,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Mardinoglu A et al. (2013). Integration of clinical data with a genome‐scale metabolic model of the human adipocyte. *Molecular Systems Biology*. [doi:10.1038/msb.2013.5](https://doi.org/10.1038/msb.2013.5), [PMID:23511207](https://pubmed.ncbi.nlm.nih.gov/23511207/) | Homo sapiens | | `MAR00015`, `MAR00016` | iAdipocytes1809 builds its lipid pool reactions from published fatty acid compositions, with plasma non-esterified fatty acids from a fasting human plasma lipidomics study that reported 31 fatty acids; fatty acids absent from that study were assigned half the lowest reported concentration. In Supplementary Dataset 8 the plasma NEFA column lists 59 fatty acids, 31 with measured values summing to 214.3 nmol/ml and the other 28 marked as not reported and given the normalised value 9e-6. | Results: Reconstruction of the adipocytes GEM iAdipocytes1809; Supplementary Dataset 8 (msb20135-s12.xlsx) | model | full text | animal-GEM | | Mardinoglu A et al. (2014). Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. *Nature Communications*. [doi:10.1038/ncomms4083](https://doi.org/10.1038/ncomms4083), [PMID:24419221](https://pubmed.ncbi.nlm.nih.gov/24419221/) | Homo sapiens | | `MAR00015`, `MAR00016` | HMR 2.0 (8,181 reactions, 6,007 metabolites, 3,765 genes) extends lipid metabolism with 59 individual fatty acids in place of a generic fatty acid pool, and the hepatocyte model iHepatocytes2322 built from it (7,930 reactions, 2,322 genes) uses the same 59 fatty acids. | Results: HMR 2.0 database | model | full text | animal-GEM | | Marill J et al. (2000). Identification of Human Cytochrome P450s Involved in the Formation of All-trans-Retinoic Acid Principal Metabolites. *Molecular Pharmacology*. [doi:10.1124/mol.58.6.1341](https://doi.org/10.1124/mol.58.6.1341) | Homo sapiens | CYP3A7, CYP3A5, CYP2C18, CYP2C8, CYP3A4, CYP2C9, CYP2B6, CYP2A6, CYP4A11, CYP1A1 | `MAR06700`, `MAR06701` | Human liver microsomes and cDNA-expressed P450s formed 4-OH-RA and 4-oxo-RA mainly via CYP3A7, then CYP3A5, 2C8, 2C18, 3A4 and 2C9 (4-OH-RA by expressed P450s, ranked by Vmax/Km); CYP2B6 and 2A6 correlated with formation in liver microsomes. CYP26 enzymes and CYP2S1 are not among the P450s tested. | Abstract | enzyme assay, expression | abstract | Human-GEM#1169, Human-GEM#1118, Human-GEM#1163 | +| Martras S et al. (2004). Kinetics of human alcohol dehydrogenase with ring-oxidized retinoids: effect of Tween 80. *Archives of Biochemistry and Biophysics*. [doi:10.1016/j.abb.2004.07.002](https://doi.org/10.1016/j.abb.2004.07.002), [PMID:15369820](https://pubmed.ncbi.nlm.nih.gov/15369820/) | Homo sapiens | ADH1B, ADH4 | `MAR20067`, `MAR20068` | Recombinant human ADH1B1, ADH1B2 and ADH4 acted on 4-hydroxyretinol with NAD+ (retinol oxidation assay) and on 4-oxoretinal with NADH (retinal reduction assay) at the highest rates of any retinoid tested (ADH4 kcat 2050 per min with 4-hydroxyretinol, a 3- to 40-fold increase over retinol and retinal). The authors state that the conversion of 4-hydroxyretinol and 4-oxoretinol to the corresponding retinoic acids has not been documented, and that oxidation of the ring of retinoic acid by P450s is well demonstrated. The paper does not show the oxidation of the ring 4-hydroxyl of 4-hydroxyretinol to 4-oxoretinol. Limits: in vitro with Tween 80, which inhibits competitively and raises Km about 10-fold | Abstract; Results (Table 1); Discussion | enzyme assay | full text | Human-GEM#1153 | | Mascarenhas R et al. (2023). Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B12 delivery and repair. *Nature Communications*. [doi:10.1038/s41467-023-40077-4](https://doi.org/10.1038/s41467-023-40077-4), [PMID:37468522](https://pubmed.ncbi.nlm.nih.gov/37468522/) | Homo sapiens | MMAA, MMAB, MMUT | | A crystal structure of the human MMUT-MMAA assembly (two MMUT chains with two MMAA dimers) shows the MMUT B12 domain rotated about 180 degrees relative to free MMUT and exposed to solvent, with MMAA wedged between the substrate and B12 domains and the interconnecting belt partially disordered. Methylmalonic aciduria mutations at the interfaces (MMUT R228Q, R616C, R694W; MMAA R98G, R209S) reduce MMUT-stimulated GTPase activation and MMAA-gated AdoCbl transfer, supporting the relevance of the structure. | Results: MMUT in the M2C2 complex; Fig. 3A | structure, enzyme assay, clinical | full text | Human-GEM#1156 | | Mathai JC et al. (2009). No facilitator required for membrane transport of hydrogen sulfide. *Proceedings of the National Academy of Sciences*. [doi:10.1073/pnas.0902952106](https://doi.org/10.1073/pnas.0902952106) | in vitro (planar lipid bilayers; archaeal aquaporin AfAQP) | | | In planar lipid bilayers, H2S permeability was at least 0.5 cm/s and did not change on reconstituting archaeal aquaporin AfAQP, which raised water permeability; the authors conclude that H2S crosses lipid membranes without a facilitator. Artificial bilayers only, H2S only (methanethiol not tested). | Abstract | metabolite measurement | abstract | Human-GEM#1133, Human-GEM#1173, Human-GEM#1174 | | Mathias MM, Sullivan AC (1981). Fatty acid and cholesterol synthesis from specifically labeled leucine by isolated rat hepatocytes. *Lipids*. [doi:10.1007/bf02535341](https://doi.org/10.1007/bf02535341) | Rattus norvegicus | | | In isolated rat hepatocytes incubated with differently labelled leucine, with and without hydroxycitrate, radioactivity from the acetyl-CoA-labelled and the acetoacetate-labelled leucine entered fatty acids and cholesterol in patterns from which the authors conclude that mitochondrial HMG-CoA is not incorporated intact into cholesterol. Rat hepatocytes only; the conclusion is drawn from tracer labelling patterns, and no transporter is examined. | Abstract | isotope tracing, metabolite measurement | abstract | Human-GEM#1173 | diff --git a/literature/registry.tsv b/literature/registry.tsv index 4103e1110..2cab7304f 100644 --- a/literature/registry.tsv +++ b/literature/registry.tsv @@ -236,3 +236,6 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1021/bi0342416 12755610 Bok D et al. 2003 Purification and Characterization of a Transmembrane Domain-Deleted Form of Lecithin Retinol Acyltransferase Biochemistry multiple LRAT MAR06639 A truncated LRAT without its transmembrane ends, expressed in E. coli with a His tag and purified, was catalytically active and processed all-trans-retinol at least ten times more efficiently than 11-cis-retinol; it forms dimers, as native LRAT does. Limits: abstract read only; the abstract does not name the species of the LRAT gene, so the organism is recorded as multiple; recombinant truncated protein extracted with detergent Abstract enzyme assay abstract Human-GEM#1149 10.1016/s0006-291x(88)80818-0 3178828 MacDonald PN et al. 1988 A lecithin: Retinol acyltransferase activity in human and rat liver Biochemical and Biophysical Research Communications Homo sapiens;Rattus norvegicus MAR06639 Human and rat liver microsomes esterified retinol bound to cellular retinol-binding protein with phosphatidylcholine as the acyl donor, and transferred little or no acyl from lysophosphatidylcholine, phosphatidylethanolamine or phosphatidic acid; only the acyl group at the sn-1 position of phosphatidylcholine was transferred. Limits: abstract read only; microsomal preparations in vitro; the enzyme and its gene were not identified Abstract enzyme assay abstract Human-GEM#1149 10.1016/s0021-9258(18)81839-7 2722792 Saari JC et al. 1989 Lecithin:Retinol Acyltransferase in Retinal Pigment Epithelial Microsomes Journal of Biological Chemistry Bos taurus MAR06639 Microsomes from retinal pigment epithelium made phosphatidylcholine from 1-palmitoyl lysophosphatidylcholine and fatty acyl-CoA, and this phosphatidylcholine served as the acyl donor for retinyl ester synthesis, which shows a lecithin:retinol acyltransferase activity; the acyl group is transferred from the 1 position of phosphatidylcholine, and the fatty acid at the 2 position matters for substrate recognition. Limits: abstract read only, and the species (bovine) is taken from the database indexing of the paper, not from the abstract; microsomes in vitro; no gene identified Abstract enzyme assay abstract Human-GEM#1149 +10.1016/0003-9861(89)90112-4 2916844 Leo MA et al. 1989 Metabolism of retinol and retinoic acid by human liver cytochrome P450IIC8 Archives of Biochemistry and Biophysics Homo sapiens CYP2C8 MAR06634 Human liver microsomes from nine subjects, and a reconstituted system with purified CYP2C8, NADPH and P450 reductase, converted retinol to 4-hydroxyretinol and other polar metabolites that were not identified (Km 0.071 mM, Vmax 1.73 nmol per min per nmol P450); purified CYP2C9 and CYP2E1 had no significant retinol hydroxylase activity, and an antibody against CYP2C8 inhibited the reaction in microsomes. The CYP2C8 system also converted retinoic acid to polar products that include 4-hydroxy- and 4-oxoretinoic acid. 4-Oxoretinol is not reported as a product of retinol. Limits: in vitro; the other polar products were not identified; CYP26A1 was not tested Abstract; Results (Table I, Fig. 1); the retinoic acid paragraph of the Results enzyme assay full text Human-GEM#1153 +10.1016/j.abb.2004.07.002 15369820 Martras S et al. 2004 Kinetics of human alcohol dehydrogenase with ring-oxidized retinoids: effect of Tween 80 Archives of Biochemistry and Biophysics Homo sapiens ADH1B;ADH4 MAR20067;MAR20068 Recombinant human ADH1B1, ADH1B2 and ADH4 acted on 4-hydroxyretinol with NAD+ (retinol oxidation assay) and on 4-oxoretinal with NADH (retinal reduction assay) at the highest rates of any retinoid tested (ADH4 kcat 2050 per min with 4-hydroxyretinol, a 3- to 40-fold increase over retinol and retinal). The authors state that the conversion of 4-hydroxyretinol and 4-oxoretinol to the corresponding retinoic acids has not been documented, and that oxidation of the ring of retinoic acid by P450s is well demonstrated. The paper does not show the oxidation of the ring 4-hydroxyl of 4-hydroxyretinol to 4-oxoretinol. Limits: in vitro with Tween 80, which inhibits competitively and raises Km about 10-fold Abstract; Results (Table 1); Discussion enzyme assay full text Human-GEM#1153 +10.1021/tx980005y 9625726 Hecht SS 1998 Biochemistry, Biology, and Carcinogenicity of Tobacco-Specific N-Nitrosamines Chemical Research in Toxicology multiple MAR07070;MAR07076 Review of the metabolism of the tobacco-specific nitrosamines. It states that keto acid is formed in vivo from keto alcohol (HPB) in rats and in some in vitro systems (cultured rat oral tissue and esophagus), that keto acid is also a likely oxidation product of keto aldehyde although this does not seem to have been investigated, and that hydroxy acid arises from NNAL by further oxidation of the lactol and the diol and not by reduction of keto acid. It names no enzyme or cofactor for these oxidations. Limits: a review that cites the underlying studies; the rat data are cited from other work Sections 2.1.1.4 (alpha-methyl hydroxylation) and 2.1.3.3 (alpha-hydroxylation) review full text Human-GEM#1153 From 6aefb9c4f14a18193c8bbbea09f32875df23ae47 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 14:08:04 +0100 Subject: [PATCH 25/44] fix: remove the gentisate aldehyde reactions MAR04702, MAR04703 and MAR04704 MAR04702 turns homogentisate into gentisate aldehyde with NADPH and O2 and has no gene or EC number; KEGG lists the reaction (R02518) as incomplete. Homogentisate is degraded by homogentisate 1,2-dioxygenase (MAR06774). MAR04703 and MAR04704 (AOX1) oxidise gentisate aldehyde, which MAR04702 alone produces, so they carry no flux without it. The three reactions go to the deprecated reactions list with their cross-references, and the gentisate aldehyde metabolite MAM01952c, which no reaction uses any more, to the deprecated metabolites list. 2,5-Dihydroxybenzoate stays in the model through MAR11900. #1153 --- .../deprecatedMetabolites.tsv | 1 + .../deprecatedReactions.tsv | 3 + model/Human-GEM.yml | 69 ------------------- model/metabolites.tsv | 1 - model/reactions.tsv | 3 - 5 files changed, 4 insertions(+), 73 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv index 1d234656b..4d5243229 100644 --- a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv +++ b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv @@ -2454,3 +2454,4 @@ MAM01267c MAM01267 HC02116 HC02116 HC02116 MNXM166880 m01267c m01267c MAM01336c MAM01336 C04295 C04295 HMDB0003818 CHEBI:2710 10634 LMST02020005 C04295 MNXM733638 C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-17,20-21H,4-11H2,1-2H3/t13-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02637 m01336c m01336c MAM01336r MAM01336 C04295 C04295 HMDB0003818 CHEBI:2710 10634 LMST02020005 C04295 MNXM733638 C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-17,20-21H,4-11H2,1-2H3/t13-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02637 m01336r m01336r MAM01336m MAM01336 C04295 C04295 HMDB0003818 CHEBI:2710 10634 LMST02020005 C04295 MNXM733638 C[C@]12CC[C@H]3[C@@H](CC=C4C[C@@H](O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H30O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-17,20-21H,4-11H2,1-2H3/t13-,14-,15-,16-,17-,18-,19-/m0/s1 cpd02637 m01336m +MAM01952c MAM01952 HC01522 C05585 HMDB0004062 CHEBI:28508 70949 HC01522 HC01522 MNXM4270 O=Cc1cc(O)ccc1O InChI=1S/C7H6O3/c8-4-5-3-6(9)1-2-7(5)10/h1-4,9-10H cpd03315 m01952c m01952c diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index e9401ee97..69e3c64ca 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -639,3 +639,6 @@ MAR05381 R02021 RE3009C RE3009C rxn05239 HMR_5381 RCR10548 0 RHEA:11724 HM MAR04188 r1332 r1332 MNXR105460 HMR_4188 RCR14479 0 HMR_4188 MAR01506 LRAT1 LRAT1 MNXR101236 0 LRAT1 MAR02313 r1253 r1253 MNXR163357 0 r1253 +MAR04702 R02518 HMR_4702 HMR_4702 MNXR107561 rxn01824 HMR_4702 RCR11362 0 HMR_4702 +MAR04703 R02655 r0558 R02655C r0558 r0558 MNXR105348 rxn01918 HMR_4703 RCR11363 0 HMR_4703 +MAR04704 R02657 r0559 R02657C r0559 r0559 MNXR105349 rxn01920 HMR_4704 RCR11364 0 HMR_4704 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e8d63faaa..e09e2722e 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -22899,13 +22899,6 @@ - charge: -2.0 - formula: C16H23N5O16P2 - metFrom: HMRdatabase - - !!omap - - id: MAM01952c - - name: gentisate aldehyde - - compartment: c - - charge: 0.0 - - formula: C7H6O3 - - metFrom: HMRdatabase - !!omap - id: MAM01953c - name: geranyl-PP @@ -72500,68 +72493,6 @@ - references: PMID:17379813;PMID:18621017 - rxnFrom: HMRdatabase - confidence_score: 0.0 - - !!omap - - id: MAR04702 - - name: homogentisate oxidative decarboxylation (gentisate aldehyde) - - metabolites: !!omap - - MAM01596c: 1.0 - - MAM01952c: 1.0 - - MAM02040c: 1.0 - - MAM02135c: -1.0 - - MAM02554c: 1.0 - - MAM02555c: -1.0 - - MAM02630c: -1.0 - - lower_bound: 0.0 - - upper_bound: 1000.0 - - subsystem: - - Tyrosine metabolism - - annotation: !!omap - - ec-code: - - 4.1.1.- - - rxnFrom: HMRdatabase - - confidence_score: 0.0 - - !!omap - - id: MAR04703 - - name: Gentisate aldehyde:NAD+ oxidoreductase - - metabolites: !!omap - - MAM00576c: 1.0 - - MAM01952c: -1.0 - - MAM02039c: 2.0 - - MAM02040c: -1.0 - - MAM02552c: -1.0 - - MAM02553c: 1.0 - - lower_bound: 0.0 - - upper_bound: 1000.0 - - gene_reaction_rule: ENSG00000138356 - - subsystem: - - Tyrosine metabolism - - annotation: !!omap - - ec-code: - - 1.2.1.29 - - references: PMID:11569919;PMID:16143537 - - rxnFrom: HMRdatabase - - confidence_score: 0.0 - - !!omap - - id: MAR04704 - - name: aldehyde oxidase (gentisate aldehyde) - - metabolites: !!omap - - MAM00576c: 1.0 - - MAM01952c: -1.0 - - MAM02039c: 1.0 - - MAM02040c: -1.0 - - MAM02041c: 1.0 - - MAM02630c: -1.0 - - lower_bound: 0.0 - - upper_bound: 1000.0 - - gene_reaction_rule: ENSG00000138356 - - subsystem: - - Tyrosine metabolism - - annotation: !!omap - - ec-code: - - 1.2.3.1 - - references: PMID:11569919;PMID:16143537 - - rxnFrom: HMRdatabase - - confidence_score: 0.0 - !!omap - id: MAR06988 - name: iodide:hydrogen-peroxide oxidoreductase diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 97f96f91e..ae7d76dda 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -3268,7 +3268,6 @@ MAM01949c MAM01949 gdpddman C01222 HMDB0001346 CHEBI:16955 439446 HC00728 gdpd MAM01950c MAM01950 gdpfuc C00325 HMDB0001095 CHEBI:17009 439211 HC00275 gdpfuc MNXM1364175 C[C@@H]1OC(OP(=O)([O-])OP(=O)([O-])OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](O)[C@@H]2O)[C@@H](O)[C@H](O)[C@@H]1O InChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/p-2/t4-,5+,7+,8+,9+,10+,11-,14+,15?/m0/s1 cpd27127 m01950c m01950c MAM01950g MAM01950 gdpfuc C00325 HMDB0001095 CHEBI:17009 439211 HC00275 gdpfuc MNXM1364175 C[C@@H]1OC(OP(=O)([O-])OP(=O)([O-])OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[C@H](O)[C@@H]2O)[C@@H](O)[C@H](O)[C@@H]1O InChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/p-2/t4-,5+,7+,8+,9+,10+,11-,14+,15?/m0/s1 cpd27127 m01950g m01950g MAM01951c MAM01951 gdpmann C00096 HMDB0001163 CHEBI:15820 18396 HC00098 gdpmann MNXM1104188 Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)([O-])OP(=O)([O-])O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H](O)[C@H]2O)c(=O)[nH]1 InChI=1S/C16H25N5O16P2/c17-16-19-12-6(13(28)20-16)18-3-21(12)14-10(26)8(24)5(34-14)2-33-38(29,30)37-39(31,32)36-15-11(27)9(25)7(23)4(1-22)35-15/h3-5,7-11,14-15,22-27H,1-2H2,(H,29,30)(H,31,32)(H3,17,19,20,28)/p-2/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1 cpd00083 m01951c m01951c -MAM01952c MAM01952 HC01522 C05585 HMDB0004062 CHEBI:28508 70949 HC01522 HC01522 MNXM4270 O=Cc1cc(O)ccc1O InChI=1S/C7H6O3/c8-4-5-3-6(9)1-2-7(5)10/h1-4,9-10H cpd03315 m01952c m01952c MAM01953c MAM01953 grdp C00341 HMDB0001285 CHEBI:17211 445995 LMPR0102010001 HC00288 grdp MNXM100 CC(C)=CCC/C(C)=C/COP(=O)([O-])OP(=O)([O-])[O-] InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/p-3/b10-7+ cpd00283 m01953c m01953c MAM01954g MAM01954 gncore1 gncore1 MNXM18091 m01954g m01954g MAM01955g MAM01955 gncore2 gncore2 MNXM18092 m01955g m01955g diff --git a/model/reactions.tsv b/model/reactions.tsv index 476ec349b..917c4ae20 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -742,9 +742,6 @@ MAR04683 R02536 ALDD19xr R02536C r0545 r0545 MNXR152946 rxn20533 HMR_4683 RCR11 MAR04685 R02536 r0546 R02536C r0546 r0546 MNXR152946 rxn20533 HMR_4685 RCR10530 0 RHEA:21393 RHEA:21392 HMR_4685 MAR04686 R02537 ALDD19x_P R02537C r0547 r0547 MNXR152944 rxn39344 HMR_4686 RCR11361 0 HMR_4686 MAR04687 R02537 r0548 R02537C r0548 r0548 MNXR152944 rxn39344 HMR_4687 RCR10531 0 HMR_4687 -MAR04702 R02518 HMR_4702 HMR_4702 MNXR107561 rxn01824 HMR_4702 RCR11362 0 HMR_4702 -MAR04703 R02655 r0558 R02655C r0558 r0558 MNXR105348 rxn01918 HMR_4703 RCR11363 0 HMR_4703 -MAR04704 R02657 r0559 R02657C r0559 r0559 MNXR105349 rxn01920 HMR_4704 RCR11364 0 HMR_4704 MAR06988 R02810 THYPX THYPX MNXR107741 rxn02022 HMR_6988 RCR14339 0 RHEA:23337 RHEA:23336 HMR_6988 MAR07689 DOPASULT DOPASULT MNXR190942 rxn27002 HMR_7689 RCR14340 0 RHEA:67881 RHEA:67880 HMR_7689 MAR07701 R07172 H2O2syn H2O2syn MNXR100492 rxn04958 HMR_7701 RCR11365 0 RHEA:11261 RHEA:11260 HMR_7701 From 765083817bb34b087c95cc9c0f08f76a72912ac2 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 14:10:59 +0100 Subject: [PATCH 26/44] feat: applyCurationTable changes reaction bounds The fields lower_bound and upper_bound are changed as floats like the charge of a metabolite. #1153 --- code/modelCuration/applyCurationTable.py | 9 +++++---- code/test/unit/test_apply_curation_table.py | 11 +++++++++++ 2 files changed, 16 insertions(+), 4 deletions(-) diff --git a/code/modelCuration/applyCurationTable.py b/code/modelCuration/applyCurationTable.py index a04ecf6a7..ce57334b6 100644 --- a/code/modelCuration/applyCurationTable.py +++ b/code/modelCuration/applyCurationTable.py @@ -7,7 +7,7 @@ (MAR), metabolite (MAM) or gene (ENSG) id, and field is one of: - name (reactions, metabolites and genes), formula and charge (metabolites), ec-code, - rxnFrom, references and gene_reaction_rule (reactions) and metabolites (reactions), in + rxnFrom, references, gene_reaction_rule, metabolites, lower_bound and upper_bound (reactions), in model/Human-GEM.yml; several EC numbers are joined by ";"; gene_reaction_rule is written with gene symbols, which the script maps to the Ensembl ids of the genes section; metabolites is a ";"-separated list of id:coefficient pairs; @@ -36,7 +36,8 @@ TSV = {"MAR": Path("model/reactions.tsv"), "MAM": Path("model/metabolites.tsv"), "ENSG": Path("model/genes.tsv")} SECTION = {"MAR": "reactions", "MAM": "metabolites", "ENSG": "genes"} -YAML_FIELDS = {"MAR": {"name", "ec-code", "rxnFrom", "references", "gene_reaction_rule", "metabolites"}, +BOUNDS = {"lower_bound", "upper_bound"} +YAML_FIELDS = {"MAR": {"name", "ec-code", "rxnFrom", "references", "gene_reaction_rule", "metabolites"} | BOUNDS, "MAM": {"name", "formula", "charge"}, "ENSG": {"name"}} # Field order of a reaction entry, as raven_toolbox.io.write_yaml_model writes it. @@ -180,7 +181,7 @@ def set(self, section: str, entry: str, field: str, value: str) -> None: pairs = [pair.rsplit(":", 1) for pair in value.split(";")] self.lines[first + 1:end] = [f" - {met}: {float(coefficient)!r}" for met, coefficient in pairs] else: - text = charge_text(value) if field == "charge" else render(value) + text = charge_text(value) if field == "charge" or field in BOUNDS else render(value) if field in blocks: first, end = blocks[field] assert end == first + 1, (entry, field) @@ -341,7 +342,7 @@ def apply(rows: list[dict], root: Path = Path(".")) -> tuple[Counter, list[str], problems.append(f"{entity}: not in {YML}") continue current = model.get(section, entity, field) - same = same_charge if field == "charge" else str.__eq__ + same = same_charge if field == "charge" or field in BOUNDS else str.__eq__ if same(current, after): continue if before is None or not same(current, before): diff --git a/code/test/unit/test_apply_curation_table.py b/code/test/unit/test_apply_curation_table.py index f0584d2ff..372df254b 100644 --- a/code/test/unit/test_apply_curation_table.py +++ b/code/test/unit/test_apply_curation_table.py @@ -190,3 +190,14 @@ def test_rule_row_is_skipped_when_a_gene_of_the_old_rule_was_deleted(root): run(root, [("MAR00002", "gene_reaction_rule", "GLYK", ""), ("ENSG00000000001", "gene", "present", "")]) changed, problems = run(root, [("MAR00002", "gene_reaction_rule", "GLYK or GONE", "")]) assert problems == [] and not changed + + +def test_bounds_changed_as_floats(root): + changed, problems = run(root, [("MAR00001", "lower_bound", "0", "-1000"), ("MAR00001", "upper_bound", "1000.0", "500")]) + assert problems == [] and changed["lower_bound"] == 1 and changed["upper_bound"] == 1 + assert " - lower_bound: -1000.0\n - upper_bound: 500.0\n" in yml(root) + + +def test_bound_that_differs_from_before_is_reported(root): + changed, problems = run(root, [("MAR00001", "lower_bound", "-5", "-1")]) + assert problems == ["MAR00001 lower_bound: '0.0', expected '-5'"] From 62302c8a65370e2fd93192fe0fec63eccd26c90f Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 14:11:15 +0100 Subject: [PATCH 27/44] fix: balance the porphyrinogen oxidations MAR04768, MAR04770 and MAR04773 The three reactions are written as the reduction of a porphyrin to the porphyrinogen with six protons, which does not balance. Porphyrinogens oxidise to the porphyrins with O2, non-enzymatically and, for uroporphyrinogen, through CYP1A2; the reactions now read porphyrinogen + 3 O2 => porphyrin + 3 H2O2 and run in that direction only. MAR04768 keeps no enzyme from the source model and gets CYP1A2, for which the evidence is limited to uroporphyrinogen and mostly to mouse. The coproporphyrinogen reactions have no gene. The change follows data/modelCuration/porphyrinogenOxidation.tsv (applyCurationTable.py); the review that supports it is in the literature registry. #1153 --- data/modelCuration/README.md | 1 + data/modelCuration/porphyrinogenOxidation.tsv | 14 +++++++ literature/registry.md | 1 + literature/registry.tsv | 1 + model/Human-GEM.yml | 40 ++++++++++--------- 5 files changed, 39 insertions(+), 18 deletions(-) create mode 100644 data/modelCuration/porphyrinogenOxidation.tsv diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index 62f2365fe..84d3ebc77 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -56,3 +56,4 @@ Static dumps of external sources that were kept here during the Human1 series (S - `pristanoylCoALumpedOxidation.tsv`: per-entity table of the change "the lumped pristanoyl-CoA oxidation counts its three cycles" (`code/modelCuration/applyCurationTable.py`). - `androstanediolHsd3b.tsv`: per-entity table of the reaction part of the change "3beta-hydroxysteroid dehydrogenase acts on 5alpha-androstane-3beta,17beta-diol" (`code/modelCuration/applyCurationTable.py`); the metabolite part was made by hand. - `stearidonicAcidLigaseDuplicate.tsv`: per-entity table of the change "MAR02982 keeps the reference and the source of its removed duplicate MAR02313" (`code/modelCuration/applyCurationTable.py`); the removal itself was made by hand. +- `porphyrinogenOxidation.tsv`: per-entity table of the change "porphyrinogens oxidise to porphyrins with O2 and H2O2 as the product, in one direction" (`code/modelCuration/applyCurationTable.py`). diff --git a/data/modelCuration/porphyrinogenOxidation.tsv b/data/modelCuration/porphyrinogenOxidation.tsv new file mode 100644 index 000000000..f8949cc8a --- /dev/null +++ b/data/modelCuration/porphyrinogenOxidation.tsv @@ -0,0 +1,14 @@ +entity field before after +MAR04768 name uroporphyrin III to uroporphyrinogen III conversion uroporphyrinogen III oxidation to uroporphyrin III +MAR04768 metabolites MAM02039c:-6.0;MAM03126c:-1.0;MAM03128c:1.0 MAM02041c:3.0;MAM02630c:-3.0;MAM03126c:1.0;MAM03128c:-1.0 +MAR04768 lower_bound -1000.0 0.0 +MAR04768 references PMID:11281297 PMID:11281297;doi:10.3390/biom16081188 +MAR04768 gene_reaction_rule CYP1A2 +MAR04770 name coproporphyrin III to coproporphyrinogen III conversion coproporphyrinogen III oxidation to coproporphyrin III +MAR04770 metabolites MAM01604c:-1.0;MAM01606c:1.0;MAM02039c:-6.0 MAM01604c:1.0;MAM01606c:-1.0;MAM02041c:3.0;MAM02630c:-3.0 +MAR04770 lower_bound -1000.0 0.0 +MAR04770 references PMID:11281297 PMID:11281297;doi:10.3390/biom16081188 +MAR04773 name coproporphyrin I to coproporphyrinogen I conversion coproporphyrinogen I oxidation to coproporphyrin I +MAR04773 metabolites MAM01603c:-1.0;MAM01605c:1.0;MAM02039c:-6.0 MAM01603c:1.0;MAM01605c:-1.0;MAM02041c:3.0;MAM02630c:-3.0 +MAR04773 lower_bound -1000.0 0.0 +MAR04773 references PMID:11281297 PMID:11281297;doi:10.3390/biom16081188 diff --git a/literature/registry.md b/literature/registry.md index f9d13c22b..8c7430569 100644 --- a/literature/registry.md +++ b/literature/registry.md @@ -205,6 +205,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Siegel D et al. (1997). The Reduction of α-Tocopherolquinone by Human NAD(P)H:Quinone Oxidoreductase: The Role of α-Tocopherolhydroquinone as a Cellular Antioxidant. *Molecular Pharmacology*. [doi:10.1124/mol.52.2.300](https://doi.org/10.1124/mol.52.2.300) | Homo sapiens | NQO1 | `MAR03047` | Purified human NQO1 reduced alpha-tocopherolquinone to the hydroquinone (Km 370 uM, kcat 5.6e3 per min) and did so more efficiently than coenzyme Q10; in CHO cells expressing human NQO1 the hydroquinone formed correlated with NQO1 activity and protected against lipid peroxidation. Purified enzyme plus a hamster cell model; the abstract does not mention CBR1 (also in the GPR). | Abstract | enzyme assay, metabolite measurement | abstract | Human-GEM | | Simpson G et al. (2000). The non-oxidative degradation of ascorbic acid at physiological conditions. *Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease*. [doi:10.1016/s0925-4439(00)00009-0](https://doi.org/10.1016/s0925-4439(00)00009-0) | in vitro chemistry | | `MAR08625` | At pH 7.0 and 37 degrees C, L-erythrulose and oxalate were the main degradation products of ascorbate, dehydroascorbate and 2,3-diketogulonate, identified by 13C NMR and HPLC; the molar yield of erythrulose from 2,3-diketogulonate was high (about 97 percent given in the abstract). Chemistry in buffer, no enzyme involved, so it supports a spontaneous reaction only in vitro. | Abstract | metabolite measurement | abstract | Human-GEM#1173 | | Singh C et al. (2017). Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m116.760744](https://doi.org/10.1074/jbc.m116.760744), [PMID:27909055](https://pubmed.ncbi.nlm.nih.gov/27909055/) | Saccharomyces cerevisiae;Homo sapiens | FGGY | `MAR08726` | Ribulose changed most in a yeast YDR109C deletion, and FGGY silencing in HEK293 cells raised ribulose (seen only with ribitol added); recombinant yeast and human FGGY preferred D-ribulose over other sugars. The authors speculate a metabolite-repair role. | Abstract | enzyme assay, knockdown phenotype, metabolite measurement | abstract | Human-GEM#1171 | +| Smith AG (2026). Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences. *Biomolecules*. [doi:10.3390/biom16081188](https://doi.org/10.3390/biom16081188), [PMID:42650854](https://pubmed.ncbi.nlm.nih.gov/42650854/) | multiple | CYP1A2 | `MAR04768`, `MAR04769`, `MAR04770`, `MAR04773` | Review of the oxidation of porphyrinogens to porphyrins. Uroporphyrinogens and coproporphyrinogens oxidise to the porphyrins in air, with iron and with reactive oxygen species, without an enzyme, and the review treats this as the usual route. In mouse, Cyp1a2 knockout prevents experimental uroporphyria, and reconstituted mouse CYP1A2 oxidises uroporphyrinogen; the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; the CYP1A2 data are from mouse and rat, and it gives no CYP1A2 data for coproporphyrinogens | Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice | review, knockout phenotype | full text | Human-GEM#1153 | | Smith G et al. (2003). Cutaneous expression of cytochrome P450 CYP2S1: individuality in regulation by therapeutic agents for psoriasis and other skin diseases. *The Lancet*. [doi:10.1016/s0140-6736(03)13081-4](https://doi.org/10.1016/s0140-6736(03)13081-4) | Homo sapiens | CYP2S1 | `MAR06700`, `MAR06701` | RT-PCR in skin of 27 healthy volunteers and 29 psoriasis patients: CYP2S1 is expressed in skin with large individual variation and is induced by UV, PUVA, coal tar and all-trans retinoic acid. The abstract reports regulation of expression, not metabolism of retinoic acid by the enzyme; the claim that CYP2S1 metabolises retinoate is not stated in the abstract and the full text was not read. | Abstract | expression, clinical | abstract | Human-GEM#1169 | | Sontag T, Parker R (2002). Cytochrome P450 omega-Hydroxylase Pathway of Tocopherol Catabolism. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m201466200](https://doi.org/10.1074/jbc.m201466200) | Homo sapiens;Rattus norvegicus | CYP4F2 | | Tocopherols are catabolised by P450 omega-hydroxylation of the phytyl chain followed by stepwise chain shortening to the 3'-carboxychromanol; intermediates of gamma-tocopherol were identified by GC-MS in hepatocyte cultures, and among recombinant human P450s only CYP4F2 had omega-hydroxylase activity, with higher activity for gamma- than alpha-tocopherol. Rat and human liver microsomes and cultured hepatocytes. | Abstract | enzyme assay, metabolite measurement | abstract | Human-GEM#1118, Human-GEM#1163 | | Suetake I et al. (2004). DNMT3L Stimulates the DNA Methylation Activity of Dnmt3a and Dnmt3b through a Direct Interaction. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m400181200](https://doi.org/10.1074/jbc.m400181200), [PMID:15105426](https://pubmed.ncbi.nlm.nih.gov/15105426/) | Mus musculus | Dnmt3l, Dnmt3a, Dnmt3b | `MAR04072`, `MAR08640`, `MAR08641` | In vitro, human DNMT3L raised the DNA methylation activity of mouse Dnmt3a and Dnmt3b 1.5- to 3-fold, increasing with the DNMT3L amount, without affecting Dnmt1, and the effect held for all DNA substrates tested, including imprinted loci, a CpG island and synthetic polynucleotides. DNMT3L bound Dnmt3a and Dnmt3b but not DNA, and the C-terminal half carried the stimulatory effect, so the authors attribute it to a direct action on catalytic activity rather than DNA targeting. | Abstract | enzyme assay | abstract | Human-GEM#1155, animal-GEM | diff --git a/literature/registry.tsv b/literature/registry.tsv index 2cab7304f..97c146ece 100644 --- a/literature/registry.tsv +++ b/literature/registry.tsv @@ -239,3 +239,4 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1016/0003-9861(89)90112-4 2916844 Leo MA et al. 1989 Metabolism of retinol and retinoic acid by human liver cytochrome P450IIC8 Archives of Biochemistry and Biophysics Homo sapiens CYP2C8 MAR06634 Human liver microsomes from nine subjects, and a reconstituted system with purified CYP2C8, NADPH and P450 reductase, converted retinol to 4-hydroxyretinol and other polar metabolites that were not identified (Km 0.071 mM, Vmax 1.73 nmol per min per nmol P450); purified CYP2C9 and CYP2E1 had no significant retinol hydroxylase activity, and an antibody against CYP2C8 inhibited the reaction in microsomes. The CYP2C8 system also converted retinoic acid to polar products that include 4-hydroxy- and 4-oxoretinoic acid. 4-Oxoretinol is not reported as a product of retinol. Limits: in vitro; the other polar products were not identified; CYP26A1 was not tested Abstract; Results (Table I, Fig. 1); the retinoic acid paragraph of the Results enzyme assay full text Human-GEM#1153 10.1016/j.abb.2004.07.002 15369820 Martras S et al. 2004 Kinetics of human alcohol dehydrogenase with ring-oxidized retinoids: effect of Tween 80 Archives of Biochemistry and Biophysics Homo sapiens ADH1B;ADH4 MAR20067;MAR20068 Recombinant human ADH1B1, ADH1B2 and ADH4 acted on 4-hydroxyretinol with NAD+ (retinol oxidation assay) and on 4-oxoretinal with NADH (retinal reduction assay) at the highest rates of any retinoid tested (ADH4 kcat 2050 per min with 4-hydroxyretinol, a 3- to 40-fold increase over retinol and retinal). The authors state that the conversion of 4-hydroxyretinol and 4-oxoretinol to the corresponding retinoic acids has not been documented, and that oxidation of the ring of retinoic acid by P450s is well demonstrated. The paper does not show the oxidation of the ring 4-hydroxyl of 4-hydroxyretinol to 4-oxoretinol. Limits: in vitro with Tween 80, which inhibits competitively and raises Km about 10-fold Abstract; Results (Table 1); Discussion enzyme assay full text Human-GEM#1153 10.1021/tx980005y 9625726 Hecht SS 1998 Biochemistry, Biology, and Carcinogenicity of Tobacco-Specific N-Nitrosamines Chemical Research in Toxicology multiple MAR07070;MAR07076 Review of the metabolism of the tobacco-specific nitrosamines. It states that keto acid is formed in vivo from keto alcohol (HPB) in rats and in some in vitro systems (cultured rat oral tissue and esophagus), that keto acid is also a likely oxidation product of keto aldehyde although this does not seem to have been investigated, and that hydroxy acid arises from NNAL by further oxidation of the lactol and the diol and not by reduction of keto acid. It names no enzyme or cofactor for these oxidations. Limits: a review that cites the underlying studies; the rat data are cited from other work Sections 2.1.1.4 (alpha-methyl hydroxylation) and 2.1.3.3 (alpha-hydroxylation) review full text Human-GEM#1153 +10.3390/biom16081188 42650854 Smith AG 2026 Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences Biomolecules multiple CYP1A2 MAR04768;MAR04769;MAR04770;MAR04773 Review of the oxidation of porphyrinogens to porphyrins. Uroporphyrinogens and coproporphyrinogens oxidise to the porphyrins in air, with iron and with reactive oxygen species, without an enzyme, and the review treats this as the usual route. In mouse, Cyp1a2 knockout prevents experimental uroporphyria, and reconstituted mouse CYP1A2 oxidises uroporphyrinogen; the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; the CYP1A2 data are from mouse and rat, and it gives no CYP1A2 data for coproporphyrinogens Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice review;knockout phenotype full text Human-GEM#1153 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e09e2722e..2c3e9c6f2 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -144510,16 +144510,18 @@ - confidence_score: 0.0 - !!omap - id: MAR04768 - - name: uroporphyrin III to uroporphyrinogen III conversion + - name: uroporphyrinogen III oxidation to uroporphyrin III - metabolites: !!omap - - MAM02039c: -6.0 - - MAM03126c: -1.0 - - MAM03128c: 1.0 - - lower_bound: -1000.0 + - MAM02041c: 3.0 + - MAM02630c: -3.0 + - MAM03126c: 1.0 + - MAM03128c: -1.0 + - lower_bound: 0.0 - upper_bound: 1000.0 + - gene_reaction_rule: ENSG00000140505 - subsystem: - Porphyrin metabolism - - references: PMID:11281297 + - references: PMID:11281297;doi:10.3390/biom16081188 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap @@ -144538,16 +144540,17 @@ - confidence_score: 0.0 - !!omap - id: MAR04770 - - name: coproporphyrin III to coproporphyrinogen III conversion + - name: coproporphyrinogen III oxidation to coproporphyrin III - metabolites: !!omap - - MAM01604c: -1.0 - - MAM01606c: 1.0 - - MAM02039c: -6.0 - - lower_bound: -1000.0 + - MAM01604c: 1.0 + - MAM01606c: -1.0 + - MAM02041c: 3.0 + - MAM02630c: -3.0 + - lower_bound: 0.0 - upper_bound: 1000.0 - subsystem: - Porphyrin metabolism - - references: PMID:11281297 + - references: PMID:11281297;doi:10.3390/biom16081188 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap @@ -144584,16 +144587,17 @@ - confidence_score: 0.0 - !!omap - id: MAR04773 - - name: coproporphyrin I to coproporphyrinogen I conversion + - name: coproporphyrinogen I oxidation to coproporphyrin I - metabolites: !!omap - - MAM01603c: -1.0 - - MAM01605c: 1.0 - - MAM02039c: -6.0 - - lower_bound: -1000.0 + - MAM01603c: 1.0 + - MAM01605c: -1.0 + - MAM02041c: 3.0 + - MAM02630c: -3.0 + - lower_bound: 0.0 - upper_bound: 1000.0 - subsystem: - Porphyrin metabolism - - references: PMID:11281297 + - references: PMID:11281297;doi:10.3390/biom16081188 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap From 8ff781d64a622242ace48c95cc062808f94f44db Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 14:11:22 +0100 Subject: [PATCH 28/44] fix: balance the NNK oxidations MAR07070 and MAR07076 without NADPH MAR07070 (4-hydroxy-1-(3-pyridinyl)-1-butanone to 3-succinoylpyridine) and MAR07076 (1-(3-pyridinyl)-1,4-butanediol to 4-hydroxy-4-(3-pyridyl)butanoate) are written with NADPH and O2 and do not balance. The in vivo conversions are reported without an enzyme or cofactor, and human lung microsomes form the keto acid without NADPH, so the reactions become the net oxidations with O2: keto alcohol + O2 => keto acid + H2O, and diol + O2 => hydroxy acid + H2O + H+. Both stay without a gene. The change follows data/modelCuration/nnkOxidationsWithoutCofactor.tsv (applyCurationTable.py). #1153 --- data/modelCuration/README.md | 1 + data/modelCuration/nnkOxidationsWithoutCofactor.tsv | 7 +++++++ model/Human-GEM.yml | 13 +++++-------- 3 files changed, 13 insertions(+), 8 deletions(-) create mode 100644 data/modelCuration/nnkOxidationsWithoutCofactor.tsv diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index 84d3ebc77..d28141873 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -57,3 +57,4 @@ Static dumps of external sources that were kept here during the Human1 series (S - `androstanediolHsd3b.tsv`: per-entity table of the reaction part of the change "3beta-hydroxysteroid dehydrogenase acts on 5alpha-androstane-3beta,17beta-diol" (`code/modelCuration/applyCurationTable.py`); the metabolite part was made by hand. - `stearidonicAcidLigaseDuplicate.tsv`: per-entity table of the change "MAR02982 keeps the reference and the source of its removed duplicate MAR02313" (`code/modelCuration/applyCurationTable.py`); the removal itself was made by hand. - `porphyrinogenOxidation.tsv`: per-entity table of the change "porphyrinogens oxidise to porphyrins with O2 and H2O2 as the product, in one direction" (`code/modelCuration/applyCurationTable.py`). +- `nnkOxidationsWithoutCofactor.tsv`: per-entity table of the change "the oxidations of the NNK metabolites 4-hydroxy-1-(3-pyridinyl)-1-butanone and 1-(3-pyridinyl)-1,4-butanediol use O2 and no NADPH" (`code/modelCuration/applyCurationTable.py`). diff --git a/data/modelCuration/nnkOxidationsWithoutCofactor.tsv b/data/modelCuration/nnkOxidationsWithoutCofactor.tsv new file mode 100644 index 000000000..59fd6d10e --- /dev/null +++ b/data/modelCuration/nnkOxidationsWithoutCofactor.tsv @@ -0,0 +1,7 @@ +entity field before after +MAR07070 name 4-hydroxy-1-(3-pyridinyl)-1-butanone hydroxylation 4-hydroxy-1-(3-pyridinyl)-1-butanone oxidation +MAR07070 metabolites MAM00917c:1.0;MAM00985c:-1.0;MAM02039c:1.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0 MAM00917c:1.0;MAM00985c:-1.0;MAM02040c:1.0;MAM02630c:-1.0 +MAR07070 references doi:10.1021/tx980005y +MAR07076 name 1-(3-pyridinyl)-1,4-butanediol hydroxylation 1-(3-pyridinyl)-1,4-butanediol oxidation +MAR07076 metabolites MAM00225c:-1.0;MAM01929c:1.0;MAM02039c:2.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0 MAM00225c:-1.0;MAM01929c:1.0;MAM02039c:1.0;MAM02040c:1.0;MAM02630c:-1.0 +MAR07076 references doi:10.1021/tx980005y diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 2c3e9c6f2..7b4f8988e 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -149819,19 +149819,17 @@ - confidence_score: 0.0 - !!omap - id: MAR07070 - - name: 4-hydroxy-1-(3-pyridinyl)-1-butanone hydroxylation + - name: 4-hydroxy-1-(3-pyridinyl)-1-butanone oxidation - metabolites: !!omap - MAM00917c: 1.0 - MAM00985c: -1.0 - - MAM02039c: 1.0 - MAM02040c: 1.0 - - MAM02554c: 1.0 - - MAM02555c: -1.0 - MAM02630c: -1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - subsystem: - Xenobiotics metabolism + - references: doi:10.1021/tx980005y - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap @@ -149908,19 +149906,18 @@ - confidence_score: 0.0 - !!omap - id: MAR07076 - - name: 1-(3-pyridinyl)-1,4-butanediol hydroxylation + - name: 1-(3-pyridinyl)-1,4-butanediol oxidation - metabolites: !!omap - MAM00225c: -1.0 - MAM01929c: 1.0 - - MAM02039c: 2.0 + - MAM02039c: 1.0 - MAM02040c: 1.0 - - MAM02554c: 1.0 - - MAM02555c: -1.0 - MAM02630c: -1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - subsystem: - Xenobiotics metabolism + - references: doi:10.1021/tx980005y - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap From 96733167d1ce879ea7ad2e094df2c1dc26f4c2ec Mon Sep 17 00:00:00 2001 From: edkerk <7326655+edkerk@users.noreply.github.com> Date: Sun, 1 Nov 2026 13:32:52 +0000 Subject: [PATCH 29/44] chore: update model QC results [skip ci] --- data/testResults/balance_results.csv | 107 ------------------ data/testResults/macaw_results.tsv | 20 ++-- data/testResults/memote_score.md | 10 +- data/testResults/model_qc_comment.md | 24 ++-- data/testResults/model_qc_summary.md | 22 ++-- data/testResults/qc_duplicate_reactions.csv | 2 + data/testResults/qc_structure_consistency.csv | 4 +- data/thermodynamics/reactionDeltaG.tsv | 15 ++- 8 files changed, 55 insertions(+), 149 deletions(-) diff --git a/data/testResults/balance_results.csv b/data/testResults/balance_results.csv index 84a8a1d26..5b50d8f30 100644 --- a/data/testResults/balance_results.csv +++ b/data/testResults/balance_results.csv @@ -1,44 +1,8 @@ reaction,name,mass_imbalance,charge_imbalance -MAR00012,fatty acid-uptake pool split into fatty acids,C:16.2056;H:30.7154;R:-1,-1 -MAR00015,NEFA blood pool in split into fatty acids,C:16.222;H:30.9664;R:-1,-1 -MAR00016,NEFA blood pool out formation,C:-16.271;H:-30.8218;R:1,1 -MAR00017,SMCFA-blood-pool to butyrate conversion,C:6.5;H:13;R:-1,-1 -MAR00022,Cofactors and vitamins pool for MAR00021,C:-1903;Co:-1;Fe:-1;H:-2922;N:-514;O:-555;P:-11;S:-24;X:1,18 -MAR00031,lipid droplet formation,C:-13.4364;H:-19.2074;N:-0.0188;O:-4.4474;P:-0.02;R:-2.0826;X:1,0.0068 -MAR00035,xenobiotics pool formation,Br:-6;C:-588;Cl:-11;H:-620;N:-66;O:-209;S:-15,11 -MAR00036,arachidonate derivatives pool formation,C:-3150;H:-4860;N:-76;O:-819;P:-15;S:-23,179 -MAR00037,steroids pool formation,C:-1116;H:-1488;I:-1;N:-81;O:-299;S:-24;Se:-1,24 -MAR00477,phospholipids extracellular pool formation,C:-32;H:-61;N:-4;O:-24;P:-3;R:-5,-1 -MAR00545,acyl-CoA-CL pool (liver tissue) formation,C:-16.6164;H:-31.9336;R:1, -MAR00546,acyl-CoA-LD-TG2 pool (liver tissue) formation,C:-16.881;H:-31.9902;R:1, -MAR00547,acyl-CoA-LD-TG3 pool (liver tissue) formation,C:-17.0032;H:-32.1644;R:1, -MAR00548,acyl-CoA-LD-PC pool (liver tissue) formation,C:-16.8292;H:-31.8668;R:1, -MAR00549,acyl-CoA-LD-PE pool (liver tissue) formation,C:-17.4164;H:-31.8982;R:1, -MAR00550,acyl-CoA-LD-PS pool (liver tissue) formation,C:-17.993;H:-33.083;R:1, -MAR00551,acyl-CoA-LD-PI pool (liver tissue) formation,C:-17.595;H:-32.8888;R:1, -MAR00552,acyl-CoA-LD-SM pool (liver tissue) formation,C:-16.0152;H:-32.0204;R:1, -MAR00553,acyl-CoA-bile-PC pool formation,C:-16.881;H:-31.9902;R:1, -MAR00555,1-acylglycerol-3P-LD-TG1 pool (liver tissue) formation,C:-15.6522;H:-31.5134;R:1, -MAR00556,1-acylglycerol-3P-LD-PC pool (liver tissue) formation,C:-16.8292;H:-31.8668;R:1, -MAR00557,1-acylglycerol-3P-LD-PE pool (liver tissue) formation,C:-17.4164;H:-31.8982;R:1, -MAR00558,1-acylglycerol-3P-LD-PS pool (liver tissue) formation,C:-17.993;H:-33.083;R:1, -MAR00559,1-acylglycerol-3P-LD-PI pool (liver tissue) formation,C:-17.595;H:-32.8888;R:1, -MAR00560,1-acylglycerol-3P-LD-SM pool (liver tissue) formation,C:-16.0152;H:-32.0204;R:1, -MAR00561,1-acylglycerol-3P-bile-PC pool formation,C:-16.881;H:-31.9902;R:1, -MAR00685,fatty acid-LD-TG1 pool (liver tissue) split into fatty acids,C:15.6522;H:31.5134;R:-1, -MAR00686,fatty acid-LD-TG2 pool (liver tissue) split into fatty acids,C:16.881;H:31.9902;R:-1, -MAR00687,fatty acid-LD-TG3 pool (liver tissue) split into fatty acids,C:17.0032;H:32.1644;R:-1, -MAR00688,fatty acid-LD-PC pool (liver tissue) split into fatty acids,C:16.8292;H:31.8668;R:-1, -MAR00689,fatty acid-LD-PE pool (liver tissue) split into fatty acids,C:17.4164;H:31.8982;R:-1, -MAR00690,fatty acid-LD-PS pool (liver tissue) split into fatty acids,C:17.993;H:33.083;R:-1, -MAR00691,fatty acid-LD-PI pool (liver tissue) split into fatty acids,C:17.595;H:32.8888;R:-1, -MAR00692,fatty acid-LD-SM pool (liver tissue) split into fatty acids,C:16.0152;H:32.0204;R:-1, MAR01065,"3-hydroxyacyl-CoA dehydrogenase (11,12-EET)",,-2 MAR01067,"3-hydroxyacyl-CoA dehydrogenase (7,8-epoxy-(4Z,10Z)-hexadecadienoic acid)",,-2 MAR01068,"3-hydroxyacyl-CoA dehydrogenase (14,15-EET)",,-2 MAR01079,fatty acid amide hydrolase (arachidonate),,-4 -MAR01185,(2E)-dodecenoyl-CoA formation (4(R)-hydroxy-dodec-(6Z)-enoate),,2 -MAR01227,(2E)-dodecenoyl-CoA formation (4(S)-hydroxy-dodec-(6Z)-enoate),,2 MAR01301,acetyl-CoA C-acyltransferase (16e-18-oxo-18-CoA-dinor-LTE4),,5 MAR01302,choloyl-CoA hydrolase (omega-COOH-tetranor-LTE3-CoA),,-3 MAR01303,acyl-CoA oxidase (omega-COOH-tetranor-LTE3-CoA),,-3 @@ -64,29 +28,7 @@ MAR01419,4-hydroperoxy-H4-neuroprostane to 4-hydroxy-E4-neuroprostane conversion MAR01427,13-hydroperoxy-H4-neuroprostane to 13-hydroxy-D4-neuroprostane conversion,,-2 MAR01430,17-hydroperoxy-H4-neuroprostane to 17-hydroxy-E4-neuroprostane conversion,,-2 MAR01431,17-hydroperoxy-H4-neuroprostane to 17-hydroxy-D4-neuroprostane conversion,,-2 -MAR01600,Peroxisomal Lumped Long Chain Fatty Acid Oxidation,,2 -MAR01932,Cholesterol:oxygen oxidoreductase (side-chain-cleaving),,-2 -MAR01934,"17alpha,20alpha-Dihydroxycholesterol:oxygen oxidoreductase (side-chain-cleaving)",,-4 -MAR01935,20alpha-Hydroxycholesterol:oxygen oxidoreductase (side-chain-cleaving),,-2 -MAR01942,cytochrome P450 (reduced ferredoxin),,-2 -MAR01950,"17alpha,21-dihydroxypregnenolone:oxygen oxidoreductase (11-hydroxylating)",,-2 -MAR01970,"steroid Delta-isomerase (5-androstene-3,17-dione)",,-2 -MAR01971,"steroid Delta-isomerase (5-androstene-3,17-dione)",,-2 -MAR02022,3beta-hydroxy-Delta(5)-steroid dehydrogenase (5-alpha-dihydrotestosterone),,2 -MAR02023,"L-Arginine, NADPH:Oxygen Oxidoreductase (Nitric-Oxide-Forming)",,1 -MAR02024,3beta-hydroxy-Delta(5)-steroid dehydrogenase (5-alpha-dihydrotestosterone),,2 -MAR02061,peroxidase (2-hydroxyestrone),,-1 -MAR02062,peroxidase (2-hydroxyestrone),,-1 -MAR02063,peroxidase (2-hydroxyestrone),,-1 -MAR02076,peroxidase (4-hydroxyestrone),,-1 -MAR02077,peroxidase (4-hydroxyestrone),,-1 -MAR02078,peroxidase (4-hydroxyestrone),,-1 MAR02091,"17beta-estradiol-3,4-semiquinone to 17beta-estradiol-3,4-quinone conversion",,-1 -MAR02099,"peroxidase (17beta-estradiol-2,3-semiquinone)",,1 -MAR02100,"peroxidase (17beta-estradiol-2,3-semiquinone)",,1 -MAR02126,stearoyl-CoA desaturase (palmitoyl-CoA),,-2 -MAR02128,stearoyl-CoA desaturase (stearoyl-CoA),,-2 -MAR02313,long-chain-fatty-acid-CoA ligase (stearidonic acid to stearoyl-CoA),,-8 MAR02443,13(S)-HPODE to 13-oxy-radical-octadecadienoate conversion,,-2 MAR02449,"12,13-epoxy-9-alkoxy-(10E)-octadecenoate hydrolysis",,-1 MAR02451,"1-hydroperoxy-8-carboxyoctyl-3,4-epoxynon-(2E)-enyl-ether to 4-oxo-2-nonenal conversion",,2 @@ -101,13 +43,8 @@ MAR03167,glutathione transferase (urate),,1 MAR03168,peptidyl-dipeptidase A (melatonin),,1 MAR03255,melatonin radical to cyclic-3-hydroxymelatonin conversion,,1 MAR03265,prostaglandin-F synthase (monodehydroascorbate),,1 -MAR03321,acyl-CoA oxidase (4-cis-decenoyl-CoA),,2 -MAR03400,3Beta-Hydroxy-Delta5-Steroid Dehydrogenase,,-2 -MAR03537,"cholesterol-ester plasma pool to cholesterol-ester-10,13,16,19-docosa conversion",C:16.764;H:31.3344;R:-1, -MAR03622,"cholesterol-ester plasma pool to cholesterol-ester-10,13,16,19-docosa conversion",C:16.764;H:31.3344;R:-1, MAR03830,"enoyl-CoA hydratase (9,10-12,13-diepoxy-octadecanoate)",,1 MAR03962,prostaglandin D2 dehydration (9-deoxy-delta12-PGD2),,-2 -MAR03992,NADH:ferricytochrome-b5 oxidoreductase,,2 MAR04007,gamma-tocopheroxyl radical hydration (8alpha-hydroxy-gamma-tocopherone),,1 MAR04015,noradrenaline to noradrenochrome conversion,,4 MAR04027,Microsomal Epoxide Hydrolase,,2 @@ -116,23 +53,11 @@ MAR04031,Microsomal Epoxide Hydrolase,,2 MAR04033,Microsomal Epoxide Hydrolase,,2 MAR04035,Microsomal Epoxide Hydrolase,,2 MAR04037,Microsomal Epoxide Hydrolase,,2 -MAR04088,Unspecific Monooxygenase,,2 -MAR04090,Unspecific Monooxygenase,,2 MAR04549,6-hydroxymelatonin-sulfate to 6-hydroxymelatonin conversion,,-2 MAR04552,hydroxide to melatonin radical conversion,,1 MAR04553,cyclic-3-hydroxymelatonin hydrolysis,,-1 -MAR04702,homogentisate oxidative decarboxylation (gentisate aldehyde),,2 MAR04763,heme oxygenase (biliverdin-producing) (hemoglobin),,1 -MAR04768,uroporphyrin III to uroporphyrinogen III conversion,,-6 MAR04769,uroporphyrin I to uroporphyrinogen III conversion,,-6 -MAR04770,coproporphyrin III to coproporphyrinogen III conversion,,-6 -MAR04773,coproporphyrin I to coproporphyrinogen I conversion,,-6 -MAR04842,SAM-dependent methyl transfer (activated methyl group pool),,-1 -MAR05155,synthesis of apo-[ACP],C:-611;H:-1000;N:-165;O:-176;R:1;S:-7, -MAR05156,synthesis of mitoApo-[ACP],C:-452;H:-708;N:-103;O:-143;R:1;S:-6, -MAR05257,fatty acid-LD-PC pool (liver tissue) split into fatty acids,C:16.8292;H:31.8668;R:-1, -MAR05266,apo-[ACP] phosphorylation,C:611;H:1000;N:165;O:176;R:-1;S:7, -MAR05267,mitoApo-[ACP] phosphorylation,C:452;H:708;N:103;O:143;R:-1;S:6, MAR06393,hydroxide to dehydroascorbic acid conversion,,1 MAR06456,gamma-tocopheroxyl-radical to gamma-tocopherol conversion,,-1 MAR06457,8alpha-hydroxy-gamma-tocopherone to gamma-tocopheroxyl-radical conversion,,-1 @@ -150,46 +75,14 @@ MAR06822,noradrenaline to noradrenochrome conversion,,4 MAR06823,crystallin zeta (noradrenochrome-O-semiquinone),,-1 MAR06881,"3,4-dihydro-1,4-benzothiazine-3-carboxylate decarboxylation",,2 MAR06885,crystallin zeta (L-dopachrome),,1 -MAR06974,[protein] to [protein]-L-lysine conversion,C:1;H:1;N:1;O:1;R:2;X:-1, -MAR06978,"release of N6,N6,N6-trimethyl-L-lysine from protein",C:-1;H:-1;N:-1;O:-1;R:-2;X:1, MAR07006,"naphthalene-1,2-diol to 1,2-naphthoquinone conversion",,2 MAR07010,"1,4-dihydroxynaphthalene to 1,4-naphthoquinone conversion",,2 -MAR07025,aflatoxin B1 dialdehyde reductase (6-propanal-forming),,-2 -MAR07026,aflatoxin B1 aldehyde reductase (6-propanal),,-2 -MAR07027,aflatoxin B1 dialdehyde reductase (6-acetaldehyde-forming),,-2 -MAR07028,aflatoxin B1 aldehyde reductase (6-acetaldehyde),,-2 MAR07046,"4-bromocatechol to 4-bromo-3,5-cyclohexadiene-1,2-dione conversion",,2 MAR07047,"bromobenzene-3,4-dihydrodiol to 4-bromocatechol conversion",,2 -MAR07070,4-hydroxy-1-(3-pyridinyl)-1-butanone hydroxylation,,2 -MAR07076,"1-(3-pyridinyl)-1,4-butanediol hydroxylation",,2 MAR07085,1-nitronaphthalene to 1-nitrosonaphthalene conversion,,-2 MAR07086,1-nitrosonaphthalene to N-hydroxy-1-aminonaphthalene conversion,,-2 MAR07087,N-hydroxy-1-aminonaphthalene to 1-naphthylamine conversion,,-2 MAR07106,S-(formylmethyl)glutathione to S-(2-hydroxyethyl)glutathione conversion,,-2 -MAR07160,Deoxynucleoside triphosphate:DNA deoxynucleotidyltransferase,C:0.2;H:5.7;N:-3.7;O:2;R:2,1 -MAR07161,nucleoside-triphosphate:RNA nucleotidyltransferase (DNA-directed),C:5.48;H:11.18;N:-3.86;O:12;P:2;R:3,-3 -MAR07162,polyribonucleotide nucleotidyltransferase (RNA),C:-5.48;H:-11.18;N:3.86;O:-12;P:-2;R:-3,3 -MAR07163,exodeoxyribonuclease III (DNA),C:-0.2;H:-5.7;N:3.7;O:-2;R:-2,-1 -MAR07164,exodeoxyribonuclease III (RNA),C:-5.48;H:-11.18;N:3.86;O:-12;P:-2;R:-3,3 -MAR07165,[protein] to [protein]-L-cysteine conversion,C:1;H:1;N:1;O:1;R:2;X:-1, -MAR07197,[protein] to [protein]-L-serine conversion,C:-3;H:-4;N:-1;O:-2, -MAR07282,[protein] to [protein]-L-asparagine conversion,C:-4;H:-5;N:-2;O:-2, -MAR07601,plasmanylethanolamine desaturase,C:2;H:4, -MAR07616,[protein] to [protein]-L-tyrosine conversion,C:1;H:1;N:1;O:1;R:2;X:-1, -MAR07621,[protein] to [protein]-L-arginine conversion,C:1;H:1;N:1;O:1;R:2;X:-1, -MAR07625,NAD+:protein-L-arginine ADP-D-ribosyltransferase,C:-1;H:-1;N:-1;O:-1;R:-2;X:1, -MAR07741,Ferredoxin:NADP+ oxidoreductase,,-2 -MAR08029,"release of N6,N6,N6-trimethyl-L-lysine from protein",C:-1;H:-1;N:-1;O:-1;R:-2;X:1, -MAR09487,NAD+:poly(adenosine diphosphate D-ribose)ADP-D-ribosyltransferase,,2 MAR09491,E2 ubiquitin-conjugating enzyme ([protein]-L-lysine),,-1 -MAR09735,[protein]-L-citrulline hydrolysis,C:-1;H:-1;N:-1;O:-1;R:-2;X:1, -MAR10033,Fatty acid pool formation and breakdown,C:16.9524;H:31.9518;R:-1, -MAR10034,Fatty acid pool formation and breakdown,C:16.9524;H:31.9518;R:-1, -MAR10035,1-acylglycerol-3-phosphate pool formation and breakdown,C:16.9524;H:31.9518;R:-1, -MAR10036,acyl-CoA pool formation and breakdown,C:16.9524;H:31.9518;R:-1, -MAR10037,cholesterol-ester pool formation and breakdown,C:16.9524;H:31.9518;R:-1, -MAR10038,cholesterol-ester pool formation and breakdown,C:16.9524;H:31.9518;R:-1, -MAR10061,fatty acyl-CoA reduction,C:-1;H:-2, MAR12995,MDZGLChr,,-1 -MAR13078,PROTEIN_BS,C:-32.5694;H:-66.0418;N:-9.3852;O:-16.5863;S:-0.283;X:1,-0.202 MAR13081,CYOOm3i,,0.06 diff --git a/data/testResults/macaw_results.tsv b/data/testResults/macaw_results.tsv index 864c4e938..ec1a63a08 100644 --- a/data/testResults/macaw_results.tsv +++ b/data/testResults/macaw_results.tsv @@ -393,6 +393,7 @@ MAR08546 MAM00013c + MAM02039c + MAM02555c <=> MAM02554c + MAM02785c MAM00013c o MAR03009 MAM02040x + MAM02774x --> MAM01597x + MAM02039x + MAM02772x MAM02772x ok ok ok N/A MAR03476 MAM01836x + MAM02040x --> MAM01597x + MAM01833x + MAM02039x MAM01833x ok ok ok N/A MAR08419 MAM00563c + MAM02348c <=> MAM00577c + MAM01597c MAM00563c ok ok ok N/A +MAR03321 MAM00980x + MAM01802x --> MAM01803x + MAM03543x ok MAR02818 ok ok N/A MAR07165 MAM00196c + MAM01628c --> MAM00200c + MAM02040c MAM00200c ok ok ok N/A MAR07166 MAM00200c + MAM01806c --> MAM02759c + MAM02898c MAM00200c;MAM02898c ok ok ok N/A MAR07167 MAM02040c + MAM02898c --> MAM00194c + MAM10009c MAM00194c;MAM02898c;MAM10009c ok ok ok N/A @@ -410,12 +411,12 @@ MAR01943 MAM02039c + MAM02555c + MAM02630c + MAM02763c --> MAM01184c + MAM02040c MAR01950 MAM00406c + 2.0 MAM02039c + MAM02630c + 2.0 MAM02828c --> MAM00283c + MAM02040c + 2.0 MAM02665c MAM00283c;MAM02665c;MAM02828c ok ok ok N/A MAR01951 MAM00283c + MAM02552c --> MAM01615c + MAM02039c + MAM02553c MAM00283c ok ok ok N/A MAR01960 MAM00408r + MAM02555r + MAM02630r --> MAM01252r + MAM01660r + MAM02040r + MAM02554r MAM01252r ok ok ok N/A -MAR02022 MAM01069c + MAM02553c <=> MAM01336c + MAM02039c + MAM02552c MAM01336c ok ok ok N/A -MAR02024 MAM01069r + MAM02553r <=> MAM01336r + MAM02039r + MAM02552r MAM01336r ok ok ok N/A +MAR02022 MAM01069c + MAM02039c + MAM02553c <=> MAM02552c + MAM20097c MAM20097c ok ok ok N/A +MAR02024 MAM01069r + MAM02039r + MAM02553r <=> MAM02552r + MAM20097r MAM20097r ok ok ok N/A MAR02050 MAM01790l + MAM02039l + MAM02555l + MAM02630l --> MAM01000l + MAM02040l + MAM02554l MAM01000l;MAM01790l;MAM02554l;MAM02555l;MAM02630l ok ok ok N/A MAR02056 MAM01790l + MAM02039l + MAM02555l + MAM02630l --> MAM00650l + MAM02040l + MAM02554l MAM00650l;MAM01790l;MAM02554l;MAM02555l;MAM02630l ok ok ok N/A -MAR02062 MAM00650l + MAM02039l + MAM02041l <=> MAM01792l + 2.0 MAM02040l MAM00650l;MAM01792l ok ok ok N/A -MAR02077 MAM01000l + MAM02039l + MAM02041l <=> MAM01794l + 2.0 MAM02040l MAM01000l;MAM01794l ok ok ok N/A +MAR02062 2.0 MAM00650l + MAM02041l <=> 2.0 MAM01792l + 2.0 MAM02040l MAM00650l;MAM01792l ok ok ok N/A +MAR02077 2.0 MAM01000l + MAM02041l <=> 2.0 MAM01794l + 2.0 MAM02040l MAM01000l;MAM01794l ok ok ok N/A MAR03537 MAM10004l --> 0.0001 MAM01452l + 0.0001 MAM01453l + 0.0001 MAM01454l + 0.0001 MAM01455l + 0.0001 MAM01456l + 0.0001 MAM01457l + 0.0001 MAM01458l + 0.0001 MAM01459l + 0.0001 MAM01460l + 0.0001 MAM01461l + 0.0001 MAM01462l + 0.0001 MAM01463l + 0.0001 MAM01464l + 0.0001 MAM01465l + 0.0041 MAM01466l + 0.0001 MAM01467l + 0.0071 MAM01468l + 0.0001 MAM01469l + 0.0001 MAM01470l + 0.0001 MAM01471l + 0.0001 MAM01472l + 0.0001 MAM01473l + 0.0001 MAM01474l + 0.0001 MAM01475l + 0.0001 MAM01476l + 0.0406 MAM01477l + 0.0001 MAM01478l + 0.0001 MAM01479l + 0.0001 MAM01480l + 0.0001 MAM01481l + 0.0001 MAM01482l + 0.0001 MAM01483l + 0.0001 MAM01484l + 0.0001 MAM01485l + 0.0001 MAM01486l + 0.0001 MAM01487l + 0.0518 MAM01488l + 0.0001 MAM01489l + 0.005 MAM01490l + 0.0001 MAM01491l + 0.0001 MAM01492l + 0.0001 MAM01493l + 0.0001 MAM01494l + 0.0001 MAM01495l + 0.0001 MAM01496l + 0.0001 MAM01497l + 0.0001 MAM01498l + 0.5254 MAM01499l + 0.0061 MAM01500l + 0.0081 MAM01501l + 0.0001 MAM01502l + 0.1958 MAM01503l + 0.138 MAM01504l + 0.0001 MAM01505l + 0.0001 MAM01506l + 0.0132 MAM01507l + 0.0001 MAM01508l + 0.0001 MAM01509l + 0.0001 MAM01510l MAM10004l ok ok ok N/A MAR03622 MAM10004r <=> 0.0001 MAM01452r + 0.0001 MAM01453r + 0.0001 MAM01454r + 0.0001 MAM01455r + 0.0001 MAM01456r + 0.0001 MAM01457r + 0.0001 MAM01458r + 0.0001 MAM01459r + 0.0001 MAM01460r + 0.0001 MAM01461r + 0.0001 MAM01462r + 0.0001 MAM01463r + 0.0001 MAM01464r + 0.0001 MAM01465r + 0.0041 MAM01466r + 0.0001 MAM01467r + 0.0071 MAM01468r + 0.0001 MAM01469r + 0.0001 MAM01470r + 0.0001 MAM01471r + 0.0001 MAM01472r + 0.0001 MAM01473r + 0.0001 MAM01474r + 0.0001 MAM01475r + 0.0001 MAM01476r + 0.0406 MAM01477r + 0.0001 MAM01478r + 0.0001 MAM01479r + 0.0001 MAM01480r + 0.0001 MAM01481r + 0.0001 MAM01482r + 0.0001 MAM01483r + 0.0001 MAM01484r + 0.0001 MAM01485r + 0.0001 MAM01486r + 0.0001 MAM01487r + 0.0518 MAM01488r + 0.0001 MAM01489r + 0.005 MAM01490r + 0.0001 MAM01491r + 0.0001 MAM01492r + 0.0001 MAM01493r + 0.0001 MAM01494r + 0.0001 MAM01495r + 0.0001 MAM01496r + 0.0001 MAM01497r + 0.0001 MAM01498r + 0.5254 MAM01499r + 0.0061 MAM01500r + 0.0081 MAM01501r + 0.0001 MAM01502r + 0.1958 MAM01503r + 0.138 MAM01504r + 0.0001 MAM01505r + 0.0001 MAM01506r + 0.0132 MAM01507r + 0.0001 MAM01508r + 0.0001 MAM01509r + 0.0001 MAM01510r MAM10004r ok ok ok N/A MAR03702 MAM01478r + MAM02040r --> MAM00115r + MAM01450r + MAM02039r MAM00115r ok ok ok N/A @@ -559,7 +560,7 @@ MAR08622 MAM00573c + MAM02040c --> MAM01596c + MAM02406c MAM02406c ok ok ok N/A MAR08623 MAM00573c + MAM02040c --> MAM01596c + MAM02424c MAM02424c ok ok ok N/A MAR08625 MAM00573c + MAM02040c --> MAM02039c + MAM02359c + MAM02661c MAM02359c ok ok ok N/A MAR04763 3.0 MAM01803c + 2.0 MAM02039c + MAM02050c + 3.0 MAM02630c --> MAM01399c + MAM01595c + 3.0 MAM01802c + MAM01822c + MAM01957c + 3.0 MAM02040c MAM01822c;MAM01957c;MAM02050c ok ok ok N/A -MAR04768 6.0 MAM02039c + MAM03126c <=> MAM03128c MAM03126c ok ok ok N/A +MAR04768 3.0 MAM02630c + MAM03128c --> 3.0 MAM02041c + MAM03126c MAM03126c ok ok ok N/A MAR09717 MAM01957c + MAM02049c --> MAM02050c MAM01957c;MAM02050c ok ok ok N/A MAR06635 MAM02684c + MAM02834c --> MAM00535c + MAM02838c MAM00535c ok ok ok N/A MAR06639 MAM00291c + MAM02684c --> MAM00535c + MAM20096c MAM00535c;MAM20096c ok ok ok N/A @@ -1248,6 +1249,7 @@ MAR02763 MAM02040l + MAM02762l <=> MAM02039l + MAM02763l + MAM02946l MAM02762l;M MAR02765 MAM01306m + MAM02319m --> MAM00990m + MAM01974m + MAM02040m MAM00990m;MAM02319m ok ok ok N/A MAR02786 MAM01371m + MAM01597m + MAM02387m --> MAM01334m + MAM02391m + MAM02759m MAM02387m ok ok ok N/A MAR02802 MAM01371x + MAM01597x + MAM02387x --> MAM01334x + MAM02391x + MAM02759x MAM02387x ok ok ok N/A +MAR02818 MAM00980x + MAM01802x --> MAM01803x + MAM03543x ok MAR03321 ok ok N/A MAR02820 MAM00081c + MAM02552c <=> MAM00855c + MAM02039c + MAM02553c MAM00081c;MAM00855c ok ok ok N/A MAR02826 MAM00696c + MAM02552c <=> MAM00854c + MAM02039c + MAM02553c MAM00696c;MAM00854c ok ok ok N/A MAR02828 MAM00082c + MAM02552c <=> MAM00883c + MAM02039c + MAM02553c MAM00082c;MAM00883c ok ok ok N/A @@ -1323,7 +1325,7 @@ MAR03391 MAM01736l + MAM02041l --> MAM01738l + 2.0 MAM02040l MAM01736l;MAM01738l MAR03392 MAM01736x + MAM02041x --> MAM01738x + 2.0 MAM02040x MAM01736x;MAM01738x ok ok ok N/A MAR03393 MAM01934r + MAM02039r + MAM02444r --> MAM00859r + MAM01596r + MAM01597r MAM00859r ok ok ok N/A MAR03394 MAM02039r + MAM02555r + MAM03029r --> MAM01697r + MAM02554r MAM03029r ok ok ok N/A -MAR03400 MAM01336m + MAM02039m + MAM02552m <=> MAM01069m + MAM02553m MAM01069m;MAM01336m ok ok ok N/A +MAR03400 MAM02552m + MAM20097m <=> MAM01069m + MAM02039m + MAM02553m MAM01069m;MAM20097m ok ok ok N/A MAR03419 MAM01675n + MAM02039n + MAM02555n --> MAM01450n + MAM02554n MAM01450n;MAM01675n ok ok ok N/A MAR03434 MAM02039r + MAM02555r + MAM03331r <=> MAM00943r + MAM02554r MAM00943r;MAM03331r ok ok ok N/A MAR03436 MAM02555m + MAM02630m + MAM03377m --> MAM01418m + MAM02040m + MAM02554m MAM01418m;MAM03377m ok ok ok N/A @@ -1410,8 +1412,8 @@ MAR04055 MAM02039r + MAM02555r + MAM02630r + MAM03382r --> MAM02040r + MAM02554r MAR04057 MAM02040c + MAM03383c --> MAM03384c MAM03383c;MAM03384c ok ok ok N/A MAR04074 MAM02040r + MAM03383r --> MAM03384r MAM03383r;MAM03384r ok ok ok N/A MAR04076 MAM02040x + MAM03383x --> MAM03384x MAM03383x;MAM03384x ok ok ok N/A -MAR04088 MAM02555c + MAM02630c + MAM03384c --> MAM02039c + MAM02040c + MAM02554c + MAM03385c MAM03384c;MAM03385c ok ok ok N/A -MAR04090 MAM02555r + MAM02630r + MAM03384r --> MAM02039r + MAM02040r + MAM02554r + MAM03385r MAM03384r;MAM03385r ok ok ok N/A +MAR04088 MAM02039c + MAM02555c + MAM02630c + MAM03384c --> MAM02040c + MAM02554c + MAM03385c MAM03384c;MAM03385c ok ok ok N/A +MAR04090 MAM02039r + MAM02555r + MAM02630r + MAM03384r --> MAM02040r + MAM02554r + MAM03385r MAM03384r;MAM03385r ok ok ok N/A MAR04154 MAM03393e <=> MAM03393e ok ok ok N/A MAR04395 MAM01428e <=> MAM01428e ok ok ok N/A MAR04397 MAM00475e <=> MAM00475e ok ok ok N/A @@ -1552,6 +1554,8 @@ MAR11815 MAM01417e --> MAM01417c ok ok MAR11964 MAR11964 N/A MAR11885 MAM01675r --> MAM01675c MAM01675r ok ok ok N/A MAR11898 MAM04074c --> MAM04074e MAM04074c;MAM04074e ok ok ok N/A MAR11899 MAM03511c --> MAM03511e MAM03511c;MAM03511e ok ok ok N/A +MAR11900 MAM00576c <=> MAM00576e MAM00576c;MAM00576e ok ok ok N/A +MAR11901 MAM00576e <=> MAM00576e ok ok ok N/A MAR11946 MAM03510c <=> MAM03510e MAM03510c;MAM03510e ok ok ok N/A MAR11964 MAM01417c --> MAM01417e ok ok MAR11815 MAR11815 N/A MAR11982 MAM04074e <=> MAM04074e ok ok ok N/A diff --git a/data/testResults/memote_score.md b/data/testResults/memote_score.md index 04b9202e6..d11ce3fa9 100644 --- a/data/testResults/memote_score.md +++ b/data/testResults/memote_score.md @@ -4,16 +4,16 @@ Mode: core subset. -Model version: 08747b00fcc6. +Model version: 49719187a1a2. Skipped (slow) tests: test_stoichiometric_consistency, test_unconserved_metabolites, test_inconsistent_min_stoichiometry, test_detect_energy_generating_cycles, test_find_stoichiometrically_balanced_cycles, test_blocked_reactions, test_find_reactions_unbounded_flux_default_condition, test_find_metabolites_not_produced_with_open_bounds, test_find_metabolites_not_consumed_with_open_bounds, test_number_independent_conservation_relations, test_matrix_rank, test_degrees_of_freedom. -**Total score: 63.8%** +**Total score: 63.9%** ### Section scores | Section | Score | | --- | ---: | -| consistency | 42.5% | +| consistency | 42.6% | | annotation_met | 77.7% | | annotation_rxn | 76.3% | | annotation_gene | 46.7% | @@ -23,8 +23,8 @@ Skipped (slow) tests: test_stoichiometric_consistency, test_unconserved_metaboli | Section | Test | Score | | --- | --- | ---: | -| Consistency | Mass Balance | 99.3% | -| Consistency | Charge Balance | 98.4% | +| Consistency | Mass Balance | 99.4% | +| Consistency | Charge Balance | 98.7% | | Consistency | Metabolite Connectivity | 100.0% | | Annotation - Metabolites | Presence of Metabolite Annotation | 100.0% | | Annotation - Metabolites | Metabolite Annotations Per Database | 47.1% | diff --git a/data/testResults/model_qc_comment.md b/data/testResults/model_qc_comment.md index c4f9843f7..a3760a95e 100644 --- a/data/testResults/model_qc_comment.md +++ b/data/testResults/model_qc_comment.md @@ -1,26 +1,22 @@ ## Model quality report -:warning: **7** pre-existing finding(s), no regressions vs `develop`. Non-blocking. Gates: duplicate keys **0** :white_check_mark:, growth **1.9** :white_check_mark:, direction alarms **0** :white_check_mark:. +:x: **3** regression(s) vs `develop`. Review the row(s) below. Gates: duplicate keys **0** :white_check_mark:, growth **1.9** :white_check_mark:, direction alarms **0** :white_check_mark:. | Section | Status | | --- | --- | -| Model & network checks (24) | :warning: **7** pre-existing | +| Model & network checks (24) | :x: **3** regression(s) | | Model file & metabolic tasks (8) | :white_check_mark: all pass | -| MEMOTE | :white_check_mark: **63.8%** (core subset) | +| MEMOTE | :sparkles: **63.9%** (core subset) | | Full report | [model_qc_summary.md](model_qc_summary.md) | -**Improved:** -- Twin reactions with a missing or conflicting EC number: **0** -- Unused genes: **0** +**Regression(s):** +- Exact-duplicate reaction groups: [**1**](qc_duplicate_reactions.csv) +- Reactions flagged as MACAW duplicates: [**340**](macaw_results.tsv) +- Reactions flagged by MACAW dead-end test: [**1382**](macaw_results.tsv) -**Pre-existing:** -- Reaction directions: warning: [**70**](qc_reversibility.csv) -- Mass-imbalanced reactions: [**65**](balance_results.csv) -- Charge-imbalanced reactions: [**145**](balance_results.csv) -- Structure vs formula/charge inconsistencies: [**51**](qc_structure_consistency.csv) -- Reactions flagged as MACAW duplicates: [**338**](macaw_results.tsv) -- Reactions flagged by MACAW dead-end test: [**1380**](macaw_results.tsv) -- Reactions split across compartments: [**26**](qc_split_compartments.csv) +**Improved:** +- Mass-imbalanced reactions: **0** +- Charge-imbalanced reactions: [**87**](balance_results.csv) :white_check_mark: unchanged · :sparkles: improved vs `develop` · :warning: pre-existing, non-blocking · :x: regression diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md index 81e6dcf30..33ff5b886 100644 --- a/data/testResults/model_qc_summary.md +++ b/data/testResults/model_qc_summary.md @@ -28,8 +28,8 @@ _Reaction directions: the alarm and the warning catch only directions that therm | --- | ---: | ---: | :---: | | [Metabolites missing formula](README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: | | [Metabolites missing charge](README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: | -| [Mass-imbalanced reactions](README.md#mass-imbalanced-reactions) | [65](balance_results.csv) | 0 | :warning: | -| [Charge-imbalanced reactions](README.md#charge-imbalanced-reactions) | [145](balance_results.csv) | 0 | :warning: | +| [Mass-imbalanced reactions](README.md#mass-imbalanced-reactions) | 0 | -65 | :sparkles: | +| [Charge-imbalanced reactions](README.md#charge-imbalanced-reactions) | [87](balance_results.csv) | -58 | :sparkles: | | [Structure vs formula/charge inconsistencies](README.md#structure-vs-formulacharge-inconsistencies) | [51](qc_structure_consistency.csv) | 0 | :warning: | #### Network structure @@ -37,14 +37,14 @@ _Reaction directions: the alarm and the warning catch only directions that therm | Check | Result | Δ vs `develop` | | | --- | ---: | ---: | :---: | | [Reactions with no metabolites](README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: | -| [Exact-duplicate reaction groups](README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: | -| [Reactions flagged as MACAW duplicates](README.md#reactions-flagged-as-macaw-duplicates) | [338](macaw_results.tsv) | 0 | :warning: | -| [Twin reactions with a missing or conflicting EC number](README.md#twin-reactions-with-a-missing-or-conflicting-ec-number) | 0 | -52 | :sparkles: | -| [Reactions flagged by MACAW dead-end test](README.md#reactions-flagged-by-macaw-dead-end-test) | [1380](macaw_results.tsv) | 0 | :warning: | +| [Exact-duplicate reaction groups](README.md#exact-duplicate-reaction-groups) | [1](qc_duplicate_reactions.csv) | +1 | :x: | +| [Reactions flagged as MACAW duplicates](README.md#reactions-flagged-as-macaw-duplicates) | [340](macaw_results.tsv) | +2 | :x: | +| [Twin reactions with a missing or conflicting EC number](README.md#twin-reactions-with-a-missing-or-conflicting-ec-number) | 0 | 0 | :white_check_mark: | +| [Reactions flagged by MACAW dead-end test](README.md#reactions-flagged-by-macaw-dead-end-test) | [1382](macaw_results.tsv) | +2 | :x: | | [Reactions split across compartments](README.md#reactions-split-across-compartments) | [26](qc_split_compartments.csv) | 0 | :warning: | | [Reaction bound / GPR issues](README.md#reaction-bound--gpr-issues) | 0 | 0 | :white_check_mark: | | [Unused metabolites](README.md#unused-metabolites) | 0 | 0 | :white_check_mark: | -| [Unused genes](README.md#unused-genes) | 0 | -2 | :sparkles: | +| [Unused genes](README.md#unused-genes) | 0 | 0 | :white_check_mark: | #### Identifiers and annotation @@ -71,11 +71,11 @@ _Reaction directions: the alarm and the warning catch only directions that therm ### [MEMOTE](README.md#memote) -**Total score: 63.8%** (core subset)   0 +**Total score: 63.9%** (core subset)   +0.1 :white_check_mark: | Section | Score | Δ vs base | | --- | ---: | ---: | -| consistency | 42.5% | 0 | +| consistency | 42.6% | +0.1 :white_check_mark: | | annotation_met | 77.7% | 0 | | annotation_rxn | 76.3% | 0 | | annotation_gene | 46.7% | 0 | @@ -85,8 +85,8 @@ _Reaction directions: the alarm and the warning catch only directions that therm | Section | Test | Score | | --- | --- | ---: | -| Consistency | Mass Balance | 99.3% | -| Consistency | Charge Balance | 98.4% | +| Consistency | Mass Balance | 99.4% | +| Consistency | Charge Balance | 98.7% | | Consistency | Metabolite Connectivity | 100.0% | | Annotation - Metabolites | Presence of Metabolite Annotation | 100.0% | | Annotation - Metabolites | Metabolite Annotations Per Database | 47.1% | diff --git a/data/testResults/qc_duplicate_reactions.csv b/data/testResults/qc_duplicate_reactions.csv index c10c4ef6a..99d7215fb 100644 --- a/data/testResults/qc_duplicate_reactions.csv +++ b/data/testResults/qc_duplicate_reactions.csv @@ -1 +1,3 @@ group,reaction,equation +1,MAR02818,MAM00980x + MAM01802x --> MAM01803x + MAM03543x +1,MAR03321,MAM00980x + MAM01802x --> MAM01803x + MAM03543x diff --git a/data/testResults/qc_structure_consistency.csv b/data/testResults/qc_structure_consistency.csv index 5af47ff90..4408f7b2a 100644 --- a/data/testResults/qc_structure_consistency.csv +++ b/data/testResults/qc_structure_consistency.csv @@ -25,8 +25,8 @@ MAM01674m,dephospho-CoA,protonation,C21H33N7O13P2S,-2.0,C21H35N7O13P2S,0,CC(C)(C MAM01966c,"glucose-1,6-bisphosphate",protonation,C6H10O12P2,-4.0,C6H14O12P2,0,O=P(O)(O)OC[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H]1O MAM01966e,"glucose-1,6-bisphosphate",protonation,C6H10O12P2,-4.0,C6H14O12P2,0,O=P(O)(O)OC[C@H]1O[C@H](OP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H]1O MAM02151c,hydroxymethylbilane,protonation,C40H38N4O17,-8.0,C40H46N4O17,0,O=C(O)CCc1c[nH]c(Cc2[nH]c(Cc3[nH]c(Cc4[nH]c(CO)c(CC(=O)O)c4CCC(=O)O)c(CC(=O)O)c3CCC(=O)O)c(CC(=O)O)c2CCC(=O)O)c1CC(=O)O -MAM02357c,lepidimoide,formula_error,X,0.0,C12H17NaO10,0,C[C@@H]1O[C@H](O)[C@H](O[C@H]2OC(C(=O)[O-])=C[C@H](O)[C@H]2O)[C@H](O)[C@H]1O.[Na+] -MAM02357e,lepidimoide,formula_error,X,0.0,C12H17NaO10,0,C[C@@H]1O[C@H](O)[C@H](O[C@H]2OC(C(=O)[O-])=C[C@H](O)[C@H]2O)[C@H](O)[C@H]1O.[Na+] +MAM02357c,lepidimoide,formula_error,C12H17O10,-1.0,C12H17NaO10,0,C[C@@H]1O[C@H](O)[C@H](O[C@H]2OC(C(=O)[O-])=C[C@H](O)[C@H]2O)[C@H](O)[C@H]1O.[Na+] +MAM02357e,lepidimoide,formula_error,C12H17O10,-1.0,C12H17NaO10,0,C[C@@H]1O[C@H](O)[C@H](O[C@H]2OC(C(=O)[O-])=C[C@H](O)[C@H]2O)[C@H](O)[C@H]1O.[Na+] MAM02441c,malonic-dialdehyde,protonation,C3H3O2,-1.0,C3H4O2,0,O=CCC=O MAM02474c,methylarsonate,protonation,CH4AsO3,-1.0,CH5AsO3,0,C[As](=O)(O)O MAM02489c,monodehydroascorbate,protonation,C6H6O6,-1.0,C6H7O6,0,[O]C1=C(O)C(=O)O[C@@H]1[C@@H](O)CO diff --git a/data/thermodynamics/reactionDeltaG.tsv b/data/thermodynamics/reactionDeltaG.tsv index abb16f2ed..b2c66f664 100644 --- a/data/thermodynamics/reactionDeltaG.tsv +++ b/data/thermodynamics/reactionDeltaG.tsv @@ -757,6 +757,8 @@ MAR01963 c single 141.9 70714.9 7118496e78 MAR01967 c single -2.3 1.6 5e7f8da44f MAR01968 r single -2.3 1.6 fb3b1c6f6a MAR01969 c single -249.8 70714.2 1b3d94ecfb +MAR01970 c single 1.7 0.9 1039c05720 +MAR01971 r single 1.7 0.9 8b3956ce5d MAR01973 c single -1.0 0.9 4248afe33f MAR01974 r single -1.0 0.9 f910c0ddf3 MAR01976 c single -14.4 8.1 a4d25defed @@ -796,6 +798,9 @@ MAR02018 c single 2.4 1.6 02a4ee8af7 MAR02019 r single 2.4 1.6 0c3a5dcc2a MAR02020 c single 141.9 70714.9 bca22d7ca8 MAR02021 e single -56.7 3.8 b72444b6c8 +MAR02022 c single 2.3 1.6 64c93a4c3a +MAR02023 c single -1221.9 15.1 77a764f643 +MAR02024 r single 2.3 1.6 1ec2faca2d MAR02025 c single -141.9 70714.9 2082ba7458 MAR02026 r single -157.1 7.8 8839abbba2 MAR02028 m single -56.1 2.1 b1f3c43358 @@ -1454,6 +1459,7 @@ MAR03393 r single -1.2 3.4 cfbde7033c MAR03394 r single -57.9 1.4 018152d7ae MAR03395 r single -57.9 1.4 5820d76bed MAR03399 r single -1.2 3.4 f4c1064632 +MAR03400 m single -7.1 1.6 51732b1dac MAR03401 r single -17.4 1.0 22cfc878af MAR03402 r single -0.4 1.5 355f0e4747 MAR03403 r single -57.9 1.4 286158d1fb @@ -2264,8 +2270,6 @@ MAR04694 c single -37.9 3.3 b7099e3f64 MAR04695 c single -9.9 3.4 b324e17c09 MAR04699 c single 6.8 141426.0 ad6409ba9b MAR04701 c single 14.0 141427.8 1c9c956d58 -MAR04703 c single -40.4 1.1 ccf97e0add -MAR04704 c single -171.6 4.3 a89da72153 MAR04705 c single -28.7 2.2 84ad818943 MAR04706 c single -45.6 2.5 e2dae3b270 MAR04707 c single -2.8 1.7 1ce238dca8 @@ -2309,8 +2313,11 @@ MAR04759 c single 3.7 1.7 bf0e5eda69 MAR04764 c single 22.0 9.9 a9cbcaa95c MAR04766 r single 8.1 5.1 079f7c2185 MAR04767 r single -0.0 0.0 677f7242b1 +MAR04768 c single -0.0 100000.0 d2a9d07549 +MAR04770 c single -0.0 100000.0 18ff4ea1a4 MAR04771 c single -314.0 400035.1 3e98478f19 MAR04772 c single -97.7 12.4 2c75539da1 +MAR04773 c single -0.0 100000.0 2f1e1de1ed MAR04776 c single -488.7 9.5 4bb5e40c2b MAR04777 m single -488.7 9.5 09a9111e6d MAR04778 c single 47.7 7.2 f50f8e0a28 @@ -2702,6 +2709,8 @@ MAR07020 c single -736.0 62807.6 392de3f1df MAR07021 c single -736.0 62807.6 2a449713ef MAR07022 c single 370.5 62806.5 c0fef51d23 MAR07023 c single 374.7 62806.4 59aad51ced +MAR07026 c single -17.8 1.0 cf21a78018 +MAR07028 c single -17.6 1.0 48251991d4 MAR07029 c single -42.7 100000.0 7738bf5b48 MAR07030 c single -400.2 6.4 699187e157 MAR07031 c single 0.0 100000.0 9884697289 @@ -2738,11 +2747,13 @@ MAR07066 c single 41.8 100000.0 2836ee39d4 MAR07067 c single 64.8 100000.0 201660957b MAR07068 c single -17.1 100000.0 5ce1f2d65c MAR07069 c single -17.1 100000.0 a7ef577fe3 +MAR07070 c single -458.3 3.1 a26e21451d MAR07071 c single -17.1 100000.0 1653bc8f0b MAR07072 c single -477.6 3.1 5d3a8b028c MAR07073 c single -17.1 100000.0 925333e60c MAR07074 c single -494.3 4.3 d831f426e6 MAR07075 c single -17.1 100000.0 8bf2795140 +MAR07076 c single -458.2 3.1 c8e1eed2b2 MAR07077 c single -17.1 100000.0 5496dc9a25 MAR07078 c single 64.8 100000.0 394b0c8353 MAR07079 c single 17.1 100000.0 db0c22f4f0 From 0320729cb1e7d6cc0bd6f8c4ebb58ccc48723abc Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:22:10 +0100 Subject: [PATCH 30/44] fix: remove MAR02818, the Recon3D duplicate of the peroxisomal 4-cis-decenoyl-CoA oxidase MAR03321 MAR02818 and MAR03321 are the same reaction in the peroxisome with the same genes (ACOX1, ACOX3) and bounds. MAR03321 is the acyl-CoA oxidase (EC 1.3.3.6) with the specific subsystem; MAR02818 carried the name and EC number of a long-chain acyl-CoA dehydrogenase (1.3.8.8). MAR03321 now also holds the two references and the source Recon3D of MAR02818, and its Recon3D and BiGG identifiers; the other cross-references of MAR02818 stay in the deprecated list. The reference and identifier changes follow data/modelCuration/acylCoAOxidaseDuplicate.tsv (applyCurationTable.py); the removal was made by hand. #1153 --- .../deprecatedReactions.tsv | 1 + data/modelCuration/README.md | 1 + .../modelCuration/acylCoAOxidaseDuplicate.tsv | 5 ++++ model/Human-GEM.yml | 23 ++----------------- model/reactions.tsv | 3 +-- 5 files changed, 10 insertions(+), 23 deletions(-) create mode 100644 data/modelCuration/acylCoAOxidaseDuplicate.tsv diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 69e3c64ca..67c39ee8e 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -642,3 +642,4 @@ MAR02313 r1253 r1253 MNXR163357 0 r1253 MAR04702 R02518 HMR_4702 HMR_4702 MNXR107561 rxn01824 HMR_4702 RCR11362 0 HMR_4702 MAR04703 R02655 r0558 R02655C r0558 r0558 MNXR105348 rxn01918 HMR_4703 RCR11363 0 HMR_4703 MAR04704 R02657 r0559 R02657C r0559 r0559 MNXR105349 rxn01920 HMR_4704 RCR11364 0 HMR_4704 +MAR02818 RE1519X;FAOXC101C102x RE1519X;FAOXC101C102x 0 RE1519X;FAOXC101C102x;MAR04966 diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index d28141873..b7c2f0bcd 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -58,3 +58,4 @@ Static dumps of external sources that were kept here during the Human1 series (S - `stearidonicAcidLigaseDuplicate.tsv`: per-entity table of the change "MAR02982 keeps the reference and the source of its removed duplicate MAR02313" (`code/modelCuration/applyCurationTable.py`); the removal itself was made by hand. - `porphyrinogenOxidation.tsv`: per-entity table of the change "porphyrinogens oxidise to porphyrins with O2 and H2O2 as the product, in one direction" (`code/modelCuration/applyCurationTable.py`). - `nnkOxidationsWithoutCofactor.tsv`: per-entity table of the change "the oxidations of the NNK metabolites 4-hydroxy-1-(3-pyridinyl)-1-butanone and 1-(3-pyridinyl)-1,4-butanediol use O2 and no NADPH" (`code/modelCuration/applyCurationTable.py`). +- `acylCoAOxidaseDuplicate.tsv`: per-entity table of the change "MAR03321 keeps the references, the source and the Recon3D identifiers of its removed duplicate MAR02818" (`code/modelCuration/applyCurationTable.py`); the removal itself was made by hand. diff --git a/data/modelCuration/acylCoAOxidaseDuplicate.tsv b/data/modelCuration/acylCoAOxidaseDuplicate.tsv new file mode 100644 index 000000000..1f4266aea --- /dev/null +++ b/data/modelCuration/acylCoAOxidaseDuplicate.tsv @@ -0,0 +1,5 @@ +entity field before after +MAR03321 references PMID:8973539;PMID:10407780;PMID:11356167 PMID:8973539;PMID:10407780;PMID:11356167;PMID:18536048;PMID:17458872 +MAR03321 rxnFrom HMRdatabase HMRdatabase;Recon3D +MAR03321 rxnBiGGID RE1519X;FAOXC101C102x +MAR03321 rxnRecon3DID HMR_3321 HMR_3321;RE1519X;FAOXC101C102x diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 7b4f8988e..3b698fa74 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -108221,8 +108221,8 @@ - annotation: !!omap - ec-code: - 1.3.3.6 - - references: PMID:8973539;PMID:10407780;PMID:11356167 - - rxnFrom: HMRdatabase + - references: PMID:8973539;PMID:10407780;PMID:11356167;PMID:18536048;PMID:17458872 + - rxnFrom: HMRdatabase;Recon3D - confidence_score: 0.0 - !!omap - id: MAR03323 @@ -206415,25 +206415,6 @@ - references: PMID:10407780;PMID:11356167;PMID:8973539 - rxnFrom: Recon3D;HMRdatabase - confidence_score: 0.0 - - !!omap - - id: MAR02818 - - name: long-chain-acyl-CoA dehydrogenase (4-cis-decenoyl-CoA) - - metabolites: !!omap - - MAM00980x: -1.0 - - MAM01802x: -1.0 - - MAM01803x: 1.0 - - MAM03543x: 1.0 - - lower_bound: 0.0 - - upper_bound: 1000.0 - - gene_reaction_rule: ENSG00000087008 or ENSG00000161533 - - subsystem: - - Fatty acid oxidation - - annotation: !!omap - - ec-code: - - 1.3.8.8 - - references: PMID:10407780;PMID:11356167;PMID:8973539;PMID:18536048;PMID:17458872 - - rxnFrom: Recon3D - - confidence_score: 0.0 - !!omap - id: MAR02820 - name: 3-hydroxyacyl-CoA dehydrogenase diff --git a/model/reactions.tsv b/model/reactions.tsv index 917c4ae20..9ae3bf62e 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2570,7 +2570,7 @@ MAR03316 R04756 FAOXC122x;RE1573X RE1573X HMR_3316;RE1573X MNXR189175 rxn03254 MAR03317 RE1520X RE1520X RE1520X MNXR162458 HMR_3317 RCR12617 0 HMR_3317 MAR03319 RE1527X RE1527X RE1527X MNXR103517 HMR_3319 RCR12618 0 HMR_3319 MAR03320 RE1534X RE1534X RE1534X HMR_3320 RCR12619 0 HMR_3320 -MAR03321 RE1519X HMR_3321 HMR_3321 RCR12620 0 HMR_3321 +MAR03321 RE1519X;FAOXC101C102x RE1519X HMR_3321;RE1519X;FAOXC101C102x HMR_3321 RCR12620 0 HMR_3321 MAR03323 FAOXC101x FAOXC101x MNXR151253 rxn44585 HMR_3323 RCR14522 0 RHEA:45755 RHEA:45752 HMR_3323 MAR03107 HMR_3107 HMR_3107 MNXR158620 HMR_3107 RCR12621 0 HMR_3107 MAR03108 HMR_3108 HMR_3108 MNXR146262 HMR_3108 RCR12622 0 HMR_3108 @@ -8438,7 +8438,6 @@ MAR02802 RE1514X MNXR153482 rxn25762 0 RHEA:33652 RHEA:33651 RE1514X MAR02804 RE1516X RE1516X RE1516X HMR_3301 RCR12606 0 RE1516X;HMR_3301 MAR02808 RE1517X RE1517X RE1517X MNXR162456 HMR_3306 RCR12610 0 RE1517X;HMR_3306;MAR00306 MAR02810 RE1518X RE1518X RE1518X HMR_3311 RCR14519 0 RE1518X;HMR_3311;MAR03311 -MAR02818 RE1519X;FAOXC101C102x RE1519X;FAOXC101C102x 0 RE1519X;FAOXC101C102x;MAR04966 MAR02820 RE1525C RE1525C MNXR103515 0 RE1525C MAR02826 RE1526C RE1526C MNXR103516 0 RE1526C MAR02828 RE1527C RE1527C MNXR103517 0 RE1527C From 18ecba5d8993ee80abf2afaf7f60cf54d69ad974 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:26:11 +0100 Subject: [PATCH 31/44] fix: the 17beta-estradiol-3,4-semiquinone is a radical with one H more than the quinone MAM00413 had the formula of the quinone (C18H22O3), so its peroxidase reactions MAR02088 and MAR02089 balanced only by releasing H2O2 from two water molecules, and the conversion to the quinone MAR02091 lacked a proton. The formula is now that of the 2,3-semiquinone (C18H23O3). MAR02088 and MAR02089 read 2 semiquinone + 2 H2O => 2 4-hydroxyestradiol + H2O2, as MAR02099 and MAR02100 do for the 2,3 isomer, and MAR02091 releases a proton as MAR02102 does. The change follows data/modelCuration/estradiolSemiquinone34.tsv (applyCurationTable.py). #1153 --- data/modelCuration/README.md | 1 + data/modelCuration/estradiolSemiquinone34.tsv | 6 ++++++ model/Human-GEM.yml | 13 +++++++------ 3 files changed, 14 insertions(+), 6 deletions(-) create mode 100644 data/modelCuration/estradiolSemiquinone34.tsv diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index b7c2f0bcd..8f3dc4ee0 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -59,3 +59,4 @@ Static dumps of external sources that were kept here during the Human1 series (S - `porphyrinogenOxidation.tsv`: per-entity table of the change "porphyrinogens oxidise to porphyrins with O2 and H2O2 as the product, in one direction" (`code/modelCuration/applyCurationTable.py`). - `nnkOxidationsWithoutCofactor.tsv`: per-entity table of the change "the oxidations of the NNK metabolites 4-hydroxy-1-(3-pyridinyl)-1-butanone and 1-(3-pyridinyl)-1,4-butanediol use O2 and no NADPH" (`code/modelCuration/applyCurationTable.py`). - `acylCoAOxidaseDuplicate.tsv`: per-entity table of the change "MAR03321 keeps the references, the source and the Recon3D identifiers of its removed duplicate MAR02818" (`code/modelCuration/applyCurationTable.py`); the removal itself was made by hand. +- `estradiolSemiquinone34.tsv`: per-entity table of the change "the 17beta-estradiol-3,4-semiquinone has the formula of the radical, and its peroxidase and quinone reactions follow" (`code/modelCuration/applyCurationTable.py`). diff --git a/data/modelCuration/estradiolSemiquinone34.tsv b/data/modelCuration/estradiolSemiquinone34.tsv new file mode 100644 index 000000000..616519f53 --- /dev/null +++ b/data/modelCuration/estradiolSemiquinone34.tsv @@ -0,0 +1,6 @@ +entity field before after +MAM00413c formula C18H22O3 C18H23O3 +MAM00413l formula C18H22O3 C18H23O3 +MAR02088 metabolites MAM00413c:-1.0;MAM00986c:1.0;MAM02040c:-2.0;MAM02041c:1.0 MAM00413c:-2.0;MAM00986c:2.0;MAM02040c:-2.0;MAM02041c:1.0 +MAR02089 metabolites MAM00413l:-1.0;MAM00986l:1.0;MAM02040l:-2.0;MAM02041l:1.0 MAM00413l:-2.0;MAM00986l:2.0;MAM02040l:-2.0;MAM02041l:1.0 +MAR02091 metabolites MAM00412c:1.0;MAM00413c:-1.0;MAM02630c:-1.0;MAM02631c:1.0 MAM00412c:1.0;MAM00413c:-1.0;MAM02039c:1.0;MAM02630c:-1.0;MAM02631c:1.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 3b698fa74..3b3588034 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -5226,14 +5226,14 @@ - name: 17beta-estradiol-3,4-semiquinone - compartment: c - charge: 0.0 - - formula: C18H22O3 + - formula: C18H23O3 - metFrom: HMRdatabase - !!omap - id: MAM00413l - name: 17beta-estradiol-3,4-semiquinone - compartment: l - charge: 0.0 - - formula: C18H22O3 + - formula: C18H23O3 - metFrom: HMRdatabase - !!omap - id: MAM00414c @@ -116783,8 +116783,8 @@ - id: MAR02088 - name: peroxidase (17beta-estradiol-3,4-semiquinone) - metabolites: !!omap - - MAM00413c: -1.0 - - MAM00986c: 1.0 + - MAM00413c: -2.0 + - MAM00986c: 2.0 - MAM02040c: -2.0 - MAM02041c: 1.0 - lower_bound: -1000.0 @@ -116803,8 +116803,8 @@ - id: MAR02089 - name: peroxidase (17beta-estradiol-3,4-semiquinone) - metabolites: !!omap - - MAM00413l: -1.0 - - MAM00986l: 1.0 + - MAM00413l: -2.0 + - MAM00986l: 2.0 - MAM02040l: -2.0 - MAM02041l: 1.0 - lower_bound: -1000.0 @@ -116825,6 +116825,7 @@ - metabolites: !!omap - MAM00412c: 1.0 - MAM00413c: -1.0 + - MAM02039c: 1.0 - MAM02630c: -1.0 - MAM02631c: 1.0 - lower_bound: 0.0 From 165a2fead945fb3376dfb8205a632bf9a4fd41f6 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:26:23 +0100 Subject: [PATCH 32/44] fix: the aflatoxin B1 dialcohol is the phenolate, as the other three metabolites of the chromophore The dialdehyde and the two monoalcohols are written as the 7-phenolate (charge -1) and the dialcohol was neutral, so the two monoalcohol reductions MAR07026 and MAR07028 needed two protons, one of them only to protonate the phenolate. The dialcohol is now the phenolate (C17H17O8, charge -1) and both reductions take one proton, as the dialdehyde reductions do. The SMILES and InChI of all four metabolites are the phenolate, so that they agree with the formula and charge in the structure test. The change follows data/modelCuration/aflatoxinDialcoholProtonation.tsv and aflatoxinPhenolateStructures.tsv (applyCurationTable.py). #1153 --- code/test/balanceTest.py | 9 +++++++++ code/test/unit/test_balance_test.py | 10 ++++++++++ data/modelCuration/README.md | 2 ++ data/modelCuration/aflatoxinDialcoholProtonation.tsv | 7 +++++++ data/modelCuration/aflatoxinPhenolateStructures.tsv | 7 +++++++ data/modelCuration/nnkOxidationsWithoutCofactor.tsv | 2 ++ data/modelCuration/succinoylpyridineProtonation.tsv | 7 +++++++ model/Human-GEM.yml | 8 ++++---- model/metabolites.tsv | 8 ++++---- 9 files changed, 52 insertions(+), 8 deletions(-) create mode 100644 data/modelCuration/aflatoxinDialcoholProtonation.tsv create mode 100644 data/modelCuration/aflatoxinPhenolateStructures.tsv create mode 100644 data/modelCuration/succinoylpyridineProtonation.tsv diff --git a/code/test/balanceTest.py b/code/test/balanceTest.py index 4c1fbee92..3ec619379 100644 --- a/code/test/balanceTest.py +++ b/code/test/balanceTest.py @@ -71,6 +71,13 @@ # the reactions that use it, or discard structure that only that convention # records. As with LUMPED_REACTIONS, a reaction that is merely unbalanced does # not belong here. +# Ordinary reactions filed under one of the lumped subsystems: single substrates and +# products, so that an elemental balance is defined and they are tested. +ORDINARY_IN_LUMPED_SUBSYSTEMS = { + "MAR01185": "(2E)-dodecenoyl-CoA formation from one hydroxy-dodecenoate, filed under Pool reactions", + "MAR01227": "(2E)-dodecenoyl-CoA formation from one hydroxy-dodecenoate, filed under Pool reactions", +} + CONVENTION_BRIDGES = { # X is the whole protein with the residue inside it, as in the glycosylation # and GPI networks; R2 writes the residue out, as in the other protein @@ -94,6 +101,8 @@ def _subsystems(rxn): def _is_lumped(rxn): """Whether the reaction stands for a whole class of species at once.""" + if rxn.id in ORDINARY_IN_LUMPED_SUBSYSTEMS: + return False return rxn.id in LUMPED_REACTIONS or bool(_subsystems(rxn) & LUMPED_SUBSYSTEMS) diff --git a/code/test/unit/test_balance_test.py b/code/test/unit/test_balance_test.py index 8894e9a74..bdca894ee 100644 --- a/code/test/unit/test_balance_test.py +++ b/code/test/unit/test_balance_test.py @@ -107,3 +107,13 @@ def test_stale_bridge_entries_use_the_given_list(): assert not any(line.startswith(kept) for line in stale) assert sum(1 for line in stale if "(not in the model)" in line) == \ len(balanceTest.CONVENTION_BRIDGES) - 2 + + +def test_ordinary_reactions_in_a_lumped_subsystem_are_tested(): + for rxn_id in balanceTest.ORDINARY_IN_LUMPED_SUBSYSTEMS: + assert not balanceTest._is_lumped(_rxn(rxn_id, {_met("a", "C"): -1}, "Pool reactions")) + assert balanceTest._is_lumped(_rxn("MAR99999", {_met("a", "C"): -1}, "Pool reactions")) + + +def test_every_ordinary_entry_says_why(): + assert all(balanceTest.ORDINARY_IN_LUMPED_SUBSYSTEMS.values()) diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index 8f3dc4ee0..8d2cce196 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -60,3 +60,5 @@ Static dumps of external sources that were kept here during the Human1 series (S - `nnkOxidationsWithoutCofactor.tsv`: per-entity table of the change "the oxidations of the NNK metabolites 4-hydroxy-1-(3-pyridinyl)-1-butanone and 1-(3-pyridinyl)-1,4-butanediol use O2 and no NADPH" (`code/modelCuration/applyCurationTable.py`). - `acylCoAOxidaseDuplicate.tsv`: per-entity table of the change "MAR03321 keeps the references, the source and the Recon3D identifiers of its removed duplicate MAR02818" (`code/modelCuration/applyCurationTable.py`); the removal itself was made by hand. - `estradiolSemiquinone34.tsv`: per-entity table of the change "the 17beta-estradiol-3,4-semiquinone has the formula of the radical, and its peroxidase and quinone reactions follow" (`code/modelCuration/applyCurationTable.py`). +- `aflatoxinDialcoholProtonation.tsv`: per-entity table of the change "the aflatoxin B1 dialcohol is the phenolate, like the dialdehyde and the monoalcohols, and its two reductions take one proton" (`code/modelCuration/applyCurationTable.py`). +- `aflatoxinPhenolateStructures.tsv`: per-entity table of the change "the SMILES and InChI of the aflatoxin B1 dialdehyde and the two monoalcohols are the phenolate" (`code/modelCuration/applyCurationTable.py`). diff --git a/data/modelCuration/aflatoxinDialcoholProtonation.tsv b/data/modelCuration/aflatoxinDialcoholProtonation.tsv new file mode 100644 index 000000000..ca504787d --- /dev/null +++ b/data/modelCuration/aflatoxinDialcoholProtonation.tsv @@ -0,0 +1,7 @@ +entity field before after +MAM01156c formula C17H18O8 C17H17O8 +MAM01156c charge 0 -1 +MAM01156c metSmiles COc1cc(O)c(C(CO)C(O)CO)c2oc(=O)c3c(c12)CCC3=O COc1cc([O-])c(C(CO)C(O)CO)c2oc(=O)c3c(c12)CCC3=O +MAM01156c metInChI InChI=1S/C17H18O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4,8,11,18-19,21-22H,2-3,5-6H2,1H3 InChI=1S/C17H18O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4,8,11,18-19,21-22H,2-3,5-6H2,1H3/p-1 +MAR07026 metabolites MAM00229c:-1.0;MAM01156c:1.0;MAM02039c:-2.0;MAM02554c:1.0;MAM02555c:-1.0 MAM00229c:-1.0;MAM01156c:1.0;MAM02039c:-1.0;MAM02554c:1.0;MAM02555c:-1.0 +MAR07028 metabolites MAM01156c:1.0;MAM01318c:-1.0;MAM02039c:-2.0;MAM02554c:1.0;MAM02555c:-1.0 MAM01156c:1.0;MAM01318c:-1.0;MAM02039c:-1.0;MAM02554c:1.0;MAM02555c:-1.0 diff --git a/data/modelCuration/aflatoxinPhenolateStructures.tsv b/data/modelCuration/aflatoxinPhenolateStructures.tsv new file mode 100644 index 000000000..12af67696 --- /dev/null +++ b/data/modelCuration/aflatoxinPhenolateStructures.tsv @@ -0,0 +1,7 @@ +entity field before after +MAM00229c metSmiles COc1cc(O)c(C(CO)C(O)C=O)c2oc(=O)c3c(c12)CCC3=O COc1cc([O-])c(C(CO)C(O)C=O)c2oc(=O)c3c(c12)CCC3=O +MAM00229c metInChI InChI=1S/C17H16O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4,6,8,11,18,21-22H,2-3,5H2,1H3 InChI=1S/C17H16O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4,6,8,11,18,21-22H,2-3,5H2,1H3/p-1 +MAM01294c metSmiles COc1cc(O)c([C@@H](C=O)[C@@H](O)C=O)c2oc(=O)c3c(c12)CCC3=O COc1cc([O-])c([C@@H](C=O)[C@@H](O)C=O)c2oc(=O)c3c(c12)CCC3=O +MAM01294c metInChI InChI=1S/C17H14O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4-6,8,11,21-22H,2-3H2,1H3/t8-,11-/m0/s1 InChI=1S/C17H14O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4-6,8,11,21-22H,2-3H2,1H3/p-1/t8-,11-/m0/s1 +MAM01318c metSmiles COc1cc(O)c(C(C=O)C(O)CO)c2oc(=O)c3c(c12)CCC3=O COc1cc([O-])c(C(C=O)C(O)CO)c2oc(=O)c3c(c12)CCC3=O +MAM01318c metInChI InChI=1S/C17H16O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4-5,8,11,19,21-22H,2-3,6H2,1H3 InChI=1S/C17H16O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4-5,8,11,19,21-22H,2-3,6H2,1H3/p-1 diff --git a/data/modelCuration/nnkOxidationsWithoutCofactor.tsv b/data/modelCuration/nnkOxidationsWithoutCofactor.tsv index 59fd6d10e..75434104f 100644 --- a/data/modelCuration/nnkOxidationsWithoutCofactor.tsv +++ b/data/modelCuration/nnkOxidationsWithoutCofactor.tsv @@ -5,3 +5,5 @@ MAR07070 references doi:10.1021/tx980005y MAR07076 name 1-(3-pyridinyl)-1,4-butanediol hydroxylation 1-(3-pyridinyl)-1,4-butanediol oxidation MAR07076 metabolites MAM00225c:-1.0;MAM01929c:1.0;MAM02039c:2.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0 MAM00225c:-1.0;MAM01929c:1.0;MAM02039c:1.0;MAM02040c:1.0;MAM02630c:-1.0 MAR07076 references doi:10.1021/tx980005y +MAR07070 references doi:10.1021/tx980005y doi:10.1021/tx980005y;PMID:7585636 +MAR07076 references doi:10.1021/tx980005y doi:10.1021/tx980005y;PMID:7585636 diff --git a/data/modelCuration/succinoylpyridineProtonation.tsv b/data/modelCuration/succinoylpyridineProtonation.tsv new file mode 100644 index 000000000..3bc8ff1bf --- /dev/null +++ b/data/modelCuration/succinoylpyridineProtonation.tsv @@ -0,0 +1,7 @@ +entity field before after +MAM00917c formula C9H9NO3 C9H8NO3 +MAM00917c charge 0 -1 +MAM00917c metSmiles O=C(O)CCC(=O)c1cccnc1 O=C([O-])CCC(=O)c1cccnc1 +MAM00917c metInChI InChI=1S/C9H9NO3/c11-8(3-4-9(12)13)7-2-1-5-10-6-7/h1-2,5-6H,3-4H2,(H,12,13) InChI=1S/C9H9NO3/c11-8(3-4-9(12)13)7-2-1-5-10-6-7/h1-2,5-6H,3-4H2,(H,12,13)/p-1 +MAR07070 metabolites MAM00917c:1.0;MAM00985c:-1.0;MAM02040c:1.0;MAM02630c:-1.0 MAM00917c:1.0;MAM00985c:-1.0;MAM02039c:1.0;MAM02040c:1.0;MAM02630c:-1.0 +MAR07072 metabolites MAM00917c:1.0;MAM01025c:-1.0;MAM02039c:-1.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0 MAM00917c:1.0;MAM01025c:-1.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 3b3588034..0cfb9d06f 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -12533,8 +12533,8 @@ - id: MAM01156c - name: 6-[2,3-dihydroxy-1-(hydroxymethyl)propyl]-1,2-dihydro-7-hydroxy-9-methoxy-cyclopenta[c][1]benzopyran-3,4-dione - compartment: c - - charge: 0.0 - - formula: C17H18O8 + - charge: -1.0 + - formula: C17H17O8 - metFrom: HMRdatabase - !!omap - id: MAM01157x @@ -149092,7 +149092,7 @@ - metabolites: !!omap - MAM00229c: -1.0 - MAM01156c: 1.0 - - MAM02039c: -2.0 + - MAM02039c: -1.0 - MAM02554c: 1.0 - MAM02555c: -1.0 - lower_bound: 0.0 @@ -149132,7 +149132,7 @@ - metabolites: !!omap - MAM01156c: 1.0 - MAM01318c: -1.0 - - MAM02039c: -2.0 + - MAM02039c: -1.0 - MAM02554c: 1.0 - MAM02555c: -1.0 - lower_bound: 0.0 diff --git a/model/metabolites.tsv b/model/metabolites.tsv index ae7d76dda..4c4472397 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -427,7 +427,7 @@ MAM00226c MAM00226 C19577 CHEBI:82571 53297440 M00226 MNXM9556 CN(N=O)C(O)C MAM00227c MAM00227 C14857 HMDB0060333 CHEBI:34032 119521 M00227 MNXM6570 ClC1(Cl)CO1 InChI=1S/C2H2Cl2O/c3-2(4)1-5-2/h1H2 cpd10554 m00227c m00227c MAM00228c MAM00228 C14039 HMDB0259827 CHEBI:34031 6366 M00228 MNXM5399 C=C(Cl)Cl InChI=1S/C2H2Cl2/c1-2(3)4/h1H2 cpd09766 m00228c m00228c MAM00228e MAM00228 C14039 HMDB0259827 CHEBI:34031 6366 M00228 MNXM5399 C=C(Cl)Cl InChI=1S/C2H2Cl2/c1-2(3)4/h1H2 cpd09766 m00228s m00228s -MAM00229c MAM00229 C19591 CHEBI:233588 53297446 M00229 MNXM9522 COc1cc(O)c(C(CO)C(O)C=O)c2oc(=O)c3c(c12)CCC3=O InChI=1S/C17H16O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4,6,8,11,18,21-22H,2-3,5H2,1H3 cpd20845 m00229c m00229c +MAM00229c MAM00229 C19591 CHEBI:233588 53297446 M00229 MNXM9522 COc1cc([O-])c(C(CO)C(O)C=O)c2oc(=O)c3c(c12)CCC3=O InChI=1S/C17H16O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4,6,8,11,18,21-22H,2-3,5H2,1H3/p-1 cpd20845 m00229c m00229c MAM00230c MAM00230 CE2152 HMDB0012488 CHEBI:92568 107838 CE2152 CE2152 MNXM468573 c1ccc2c3c([nH]c2c1)C[NH2+]CC3 InChI=1S/C11H12N2/c1-2-4-10-8(3-1)9-5-6-12-7-11(9)13-10/h1-4,12-13H,5-7H2/p+1 m00230c m00230c MAM00231c MAM00231 CE5629 HMDB0012490 CHEBI:178978 20844 CE5629 CE5629 MNXM32113 CC1=NCCc2cc(O)c(O)cc21 InChI=1S/C10H11NO2/c1-6-8-5-10(13)9(12)4-7(8)2-3-11-6/h4-5,12-13H,2-3H2,1H3 m00231c m00231c MAM00232e MAM00232 C04759 MNXM91041 *NC(=O)[C@H](CC[C@H](CN)O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)NC(*)=O cpd12607 @@ -1784,7 +1784,7 @@ MAM01153r MAM01153 CE5352 CE5352 CE5352 MNXM164366 CCCCCC=CC[C@@H](O)C=CC= MAM01154c MAM01154 CE2172 HMDB0006044 CHEBI:173739 36937 CE2172 CE2172 MNXM64956 Oc1cc2c(cc1O)C[NH2+]CC2 InChI=1S/C9H11NO2/c11-8-3-6-1-2-10-5-7(6)4-9(8)12/h3-4,10-12H,1-2,5H2/p+1 m01154c m01154c MAM01155c MAM01155 ahdt C04895 HMDB0000980 CHEBI:18372 121885 HC01367 ahdt MNXM1369355 Nc1nc2c(c(=O)[nH]1)N=C([C@H](O)[C@H](O)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])CN2 InChI=1S/C9H16N5O13P3/c10-9-13-7-5(8(17)14-9)12-3(1-11-7)6(16)4(15)2-25-29(21,22)27-30(23,24)26-28(18,19)20/h4,6,15-16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H4,10,11,13,14,17)/p-4/t4-,6+/m1/s1 cpd02978 m01155c m01155c MAM01155n MAM01155 ahdt C04895 HMDB0000980 CHEBI:18372 121885 HC01367 ahdt MNXM1369355 Nc1nc2c(c(=O)[nH]1)N=C([C@H](O)[C@H](O)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])[O-])CN2 InChI=1S/C9H16N5O13P3/c10-9-13-7-5(8(17)14-9)12-3(1-11-7)6(16)4(15)2-25-29(21,22)27-30(23,24)26-28(18,19)20/h4,6,15-16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H4,10,11,13,14,17)/p-4/t4-,6+/m1/s1 cpd02978 m01155n m01155n -MAM01156c MAM01156 C19590 HMDB0062427 CHEBI:53108 53297445 M01156 MNXM10359 COc1cc(O)c(C(CO)C(O)CO)c2oc(=O)c3c(c12)CCC3=O InChI=1S/C17H18O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4,8,11,18-19,21-22H,2-3,5-6H2,1H3 cpd20844 m01156c m01156c +MAM01156c MAM01156 C19590 HMDB0062427 CHEBI:53108 53297445 M01156 MNXM10359 COc1cc([O-])c(C(CO)C(O)CO)c2oc(=O)c3c(c12)CCC3=O InChI=1S/C17H18O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4,8,11,18-19,21-22H,2-3,5-6H2,1H3/p-1 cpd20844 m01156c m01156c MAM01157x MAM01157 6a2ohxnt C03239 HMDB0012151 CHEBI:17534 439954 6a2ohxnt MNXM916 NCCCCC(=O)C(=O)O InChI=1S/C6H11NO3/c7-4-2-1-3-5(8)6(9)10/h1-4,7H2,(H,9,10) cpd02074 m01157p m01157p MAM01158c MAM01158 6htststerone C14497 HMDB0006259 CHEBI:34477 65543 LMST02020054 6htststerone MNXM1107925 C[C@]12CC[C@H]3[C@@H](C[C@@H](O)C4=CC(=O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H28O3/c1-18-7-5-11(20)9-15(18)16(21)10-12-13-3-4-17(22)19(13,2)8-6-14(12)18/h9,12-14,16-17,21-22H,3-8,10H2,1-2H3/t12-,13-,14-,16+,17-,18+,19-/m0/s1 cpd10196 m01158c m01158c MAM01158r MAM01158 6htststerone C14497 HMDB0006259 CHEBI:34477 65543 LMST02020054 6htststerone MNXM1107925 C[C@]12CC[C@H]3[C@@H](C[C@@H](O)C4=CC(=O)CC[C@@]43C)[C@@H]1CC[C@@H]2O InChI=1S/C19H28O3/c1-18-7-5-11(20)9-15(18)16(21)10-12-13-3-4-17(22)19(13,2)8-6-14(12)18/h9,12-14,16-17,21-22H,3-8,10H2,1-2H3/t12-,13-,14-,16+,17-,18+,19-/m0/s1 cpd10196 m01158r m01158r @@ -2008,7 +2008,7 @@ MAM01291r MAM01291 adrn C16527 HMDB0002226 CHEBI:53487 5497181 LMFA01030178 ad MAM01291e MAM01291 adrn C16527 HMDB0002226 CHEBI:53487 5497181 LMFA01030178 adrn MNXM1108185 CCCCC/C=C\C/C=C\C/C=C\C/C=C\CCCCCC(=O)[O-] InChI=1S/C22H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22(23)24/h6-7,9-10,12-13,15-16H,2-5,8,11,14,17-21H2,1H3,(H,23,24)/p-1/b7-6-,10-9-,13-12-,16-15- cpd16342 m01291s m01291s MAM01292c MAM01292 CE5536 CHEBI:166544 5898 CE5536 CE5536 MNXM1369372 CN1CC(O)C2=CC(=O)C(=O)C=C21 InChI=1S/C9H9NO3/c1-10-4-9(13)5-2-7(11)8(12)3-6(5)10/h2-3,9,13H,4H2,1H3 m01292c m01292c MAM01293c MAM01293 CHEBI:173854 10313383 CE5541 CE5541 MNXM1129403 CN1CC(O)c2cc([O])c([O-])cc21 InChI=1S/C9H10NO3/c1-10-4-9(13)5-2-7(11)8(12)3-6(5)10/h2-3,9,12-13H,4H2,1H3/p-1 m01293c m01293c -MAM01294c MAM01294 C19589 53297444 M01294 MNXM735521 COc1cc(O)c([C@@H](C=O)[C@@H](O)C=O)c2oc(=O)c3c(c12)CCC3=O InChI=1S/C17H14O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4-6,8,11,21-22H,2-3H2,1H3/t8-,11-/m0/s1 cpd20843 m01294c m01294c +MAM01294c MAM01294 C19589 53297444 M01294 MNXM735521 COc1cc([O-])c([C@@H](C=O)[C@@H](O)C=O)c2oc(=O)c3c(c12)CCC3=O InChI=1S/C17H14O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4-6,8,11,21-22H,2-3H2,1H3/p-1/t8-,11-/m0/s1 cpd20843 m01294c m01294c MAM01295c MAM01295 C19588 HMDB0060430 CHEBI:82580 3035008 M01295 MNXM164503 COc1cc2c(c3oc(=O)c4c(c13)CCC4=O)[C@H]1[C@@H](O2)O[C@@H](O)[C@@H]1O InChI=1S/C17H14O8/c1-22-7-4-8-11(12-13(19)16(21)25-17(12)23-8)14-10(7)5-2-3-6(18)9(5)15(20)24-14/h4,12-13,16-17,19,21H,2-3H2,1H3/t12-,13-,16-,17+/m1/s1 cpd20842 m01295c m01295c MAM01296c MAM01296 aflatoxin C06800 HMDB0006552 CHEBI:2504 186907 LMPK10000006 aflatoxin MNXM735258 COc1cc2c(c3oc(=O)c4c(c13)CCC4=O)[C@@H]1C=CO[C@@H]1O2 InChI=1S/C17H12O6/c1-20-10-6-11-14(8-4-5-21-17(8)22-11)15-13(10)7-2-3-9(18)12(7)16(19)23-15/h4-6,8,17H,2-3H2,1H3/t8-,17+/m0/s1 cpd04172 m01296c m01296c MAM01296e MAM01296 aflatoxin C06800 HMDB0006552 CHEBI:2504 186907 LMPK10000006 aflatoxin MNXM735258 COc1cc2c(c3oc(=O)c4c(c13)CCC4=O)[C@@H]1C=CO[C@@H]1O2 InChI=1S/C17H12O6/c1-20-10-6-11-14(8-4-5-21-17(8)22-11)15-13(10)7-2-3-9(18)12(7)16(19)23-15/h4-6,8,17H,2-3H2,1H3/t8-,17+/m0/s1 cpd04172 m01296s m01296s @@ -2050,7 +2050,7 @@ MAM01315e MAM01315 HMDB0002818 CHEBI:76451 5781 CE0074 CE0074 MNXM15828 O=C1 MAM01316c MAM01316 decdp C17432 CHEBI:60721 decdp MNXM1371339 CC(C)=CCC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/COP(=O)([O-])OP(=O)([O-])[O-] InChI=1S/C50H84O7P2/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-56-59(54,55)57-58(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H,54,55)(H2,51,52,53)/p-3/b42-23+,43-25+,44-27+,45-29+,46-31+,47-33+,48-35+,49-37+,50-39+ cpd19241 m01316c m01316c MAM01316m MAM01316 decdp C17432 CHEBI:60721 decdp MNXM1371339 CC(C)=CCC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC/C(C)=C/COP(=O)([O-])OP(=O)([O-])[O-] InChI=1S/C50H84O7P2/c1-41(2)21-12-22-42(3)23-13-24-43(4)25-14-26-44(5)27-15-28-45(6)29-16-30-46(7)31-17-32-47(8)33-18-34-48(9)35-19-36-49(10)37-20-38-50(11)39-40-56-59(54,55)57-58(51,52)53/h21,23,25,27,29,31,33,35,37,39H,12-20,22,24,26,28,30,32,34,36,38,40H2,1-11H3,(H,54,55)(H2,51,52,53)/p-3/b42-23+,43-25+,44-27+,45-29+,46-31+,47-33+,48-35+,49-37+,50-39+ cpd19241 m01316m m01316m MAM01317c MAM01317 C01392 M01317 MNXM739687 *[C@H](N)C(=O)N[C@@H](*)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)O cpd11859 m01317c m01317c -MAM01318c MAM01318 C19592 HMDB0062442 CHEBI:233587 53297447 M01318 MNXM10642 COc1cc(O)c(C(C=O)C(O)CO)c2oc(=O)c3c(c12)CCC3=O InChI=1S/C17H16O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4-5,8,11,19,21-22H,2-3,6H2,1H3 cpd20846 m01318c m01318c +MAM01318c MAM01318 C19592 HMDB0062442 CHEBI:233587 53297447 M01318 MNXM10642 COc1cc([O-])c(C(C=O)C(O)CO)c2oc(=O)c3c(c12)CCC3=O InChI=1S/C17H16O8/c1-24-12-4-10(21)13(8(5-18)11(22)6-19)16-15(12)7-2-3-9(20)14(7)17(23)25-16/h4-5,8,11,19,21-22H,2-3,6H2,1H3/p-1 cpd20846 m01318c m01318c MAM01319c MAM01319 C19581 HMDB0062443 CHEBI:82575 53297442 M01319 MNXM10644 O=NNCCCC(O)c1cccnc1 InChI=1S/C9H13N3O2/c13-9(4-2-6-11-12-14)8-3-1-5-10-7-8/h1,3,5,7,9,13H,2,4,6H2,(H,11,14) cpd20835 m01319c m01319c MAM01320c MAM01320 C19580 HMDB0062444 CHEBI:82574 53297441 M01320 MNXM10645 O=NN(CO)CCCC(O)c1cccnc1 InChI=1S/C10H15N3O3/c14-8-13(12-16)6-2-4-10(15)9-3-1-5-11-7-9/h1,3,5,7,10,14-15H,2,4,6,8H2 cpd20834 m01320c m01320c MAM01321c MAM01321 CE5853 CE5853 CE5853 MNXM739689 Cc1c(C)c2c(c(C)c1[O-])CCC(C)(CCC(=O)O[C@H]1O[C@@H](C(=O)O)[C@@H](O)[C@@H](O)[C@H]1O)O2 InChI=1S/C22H30O10/c1-9-10(2)18-12(11(3)14(9)24)5-7-22(4,32-18)8-6-13(23)30-21-17(27)15(25)16(26)19(31-21)20(28)29/h15-17,19,21,24-27H,5-8H2,1-4H3,(H,28,29)/p-1/t15-,16+,17-,19-,21+,22?/m1/s1 m01321c m01321c From f51e8832d35c0acb1ac87b33102f21dca6a574c6 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:26:36 +0100 Subject: [PATCH 33/44] fix: 3-succinoylpyridine is the carboxylate, as the hydroxy acid that the NNK diol forms 3-Succinoylpyridine was the neutral acid while 4-hydroxy-4-(3-pyridyl)butanoate, formed in parallel, is the carboxylate. It is now the carboxylate (C9H8NO3, charge -1) with its SMILES and InChI. MAR07070 releases a proton as MAR07076 does, and MAR07072 no longer takes one. MAR07070 and MAR07076 also cite the study of human lung microsomes (PMID:7585636). The change follows data/modelCuration/succinoylpyridineProtonation.tsv and nnkOxidationsWithoutCofactor.tsv (applyCurationTable.py). #1153 --- data/modelCuration/README.md | 1 + data/modelCuration/nnkOxidationsWithoutCofactor.tsv | 6 +++--- model/Human-GEM.yml | 10 +++++----- model/metabolites.tsv | 2 +- 4 files changed, 10 insertions(+), 9 deletions(-) diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index 8d2cce196..326e0f783 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -62,3 +62,4 @@ Static dumps of external sources that were kept here during the Human1 series (S - `estradiolSemiquinone34.tsv`: per-entity table of the change "the 17beta-estradiol-3,4-semiquinone has the formula of the radical, and its peroxidase and quinone reactions follow" (`code/modelCuration/applyCurationTable.py`). - `aflatoxinDialcoholProtonation.tsv`: per-entity table of the change "the aflatoxin B1 dialcohol is the phenolate, like the dialdehyde and the monoalcohols, and its two reductions take one proton" (`code/modelCuration/applyCurationTable.py`). - `aflatoxinPhenolateStructures.tsv`: per-entity table of the change "the SMILES and InChI of the aflatoxin B1 dialdehyde and the two monoalcohols are the phenolate" (`code/modelCuration/applyCurationTable.py`). +- `succinoylpyridineProtonation.tsv`: per-entity table of the change "3-succinoylpyridine is the carboxylate, as the hydroxy acid formed in parallel, and its two formation reactions follow" (`code/modelCuration/applyCurationTable.py`). diff --git a/data/modelCuration/nnkOxidationsWithoutCofactor.tsv b/data/modelCuration/nnkOxidationsWithoutCofactor.tsv index 75434104f..83c380880 100644 --- a/data/modelCuration/nnkOxidationsWithoutCofactor.tsv +++ b/data/modelCuration/nnkOxidationsWithoutCofactor.tsv @@ -1,9 +1,9 @@ entity field before after MAR07070 name 4-hydroxy-1-(3-pyridinyl)-1-butanone hydroxylation 4-hydroxy-1-(3-pyridinyl)-1-butanone oxidation -MAR07070 metabolites MAM00917c:1.0;MAM00985c:-1.0;MAM02039c:1.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0 MAM00917c:1.0;MAM00985c:-1.0;MAM02040c:1.0;MAM02630c:-1.0 -MAR07070 references doi:10.1021/tx980005y +MAR07070 metabolites MAM00917c:1.0;MAM00985c:-1.0;MAM02039c:1.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0 MAM00917c:1.0;MAM00985c:-1.0;MAM02039c:1.0;MAM02040c:1.0;MAM02630c:-1.0 MAR07076 name 1-(3-pyridinyl)-1,4-butanediol hydroxylation 1-(3-pyridinyl)-1,4-butanediol oxidation MAR07076 metabolites MAM00225c:-1.0;MAM01929c:1.0;MAM02039c:2.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0 MAM00225c:-1.0;MAM01929c:1.0;MAM02039c:1.0;MAM02040c:1.0;MAM02630c:-1.0 -MAR07076 references doi:10.1021/tx980005y +MAR07070 references doi:10.1021/tx980005y MAR07070 references doi:10.1021/tx980005y doi:10.1021/tx980005y;PMID:7585636 +MAR07076 references doi:10.1021/tx980005y MAR07076 references doi:10.1021/tx980005y doi:10.1021/tx980005y;PMID:7585636 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 0cfb9d06f..626796031 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -10069,8 +10069,8 @@ - id: MAM00917c - name: 3-succinoylpyridine - compartment: c - - charge: 0.0 - - formula: C9H9NO3 + - charge: -1.0 + - formula: C9H8NO3 - metFrom: HMRdatabase - !!omap - id: MAM00918c @@ -149824,13 +149824,14 @@ - metabolites: !!omap - MAM00917c: 1.0 - MAM00985c: -1.0 + - MAM02039c: 1.0 - MAM02040c: 1.0 - MAM02630c: -1.0 - lower_bound: 0.0 - upper_bound: 1000.0 - subsystem: - Xenobiotics metabolism - - references: doi:10.1021/tx980005y + - references: doi:10.1021/tx980005y;PMID:7585636 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap @@ -149852,7 +149853,6 @@ - metabolites: !!omap - MAM00917c: 1.0 - MAM01025c: -1.0 - - MAM02039c: -1.0 - MAM02040c: 1.0 - MAM02554c: 1.0 - MAM02555c: -1.0 @@ -149918,7 +149918,7 @@ - upper_bound: 1000.0 - subsystem: - Xenobiotics metabolism - - references: doi:10.1021/tx980005y + - references: doi:10.1021/tx980005y;PMID:7585636 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 4c4472397..544fda5e0 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -1432,7 +1432,7 @@ MAM00913m MAM00913 3pg C00197 HMDB0000807 CHEBI:17794 439183 HC00186 3pg MNXM7 MAM00914c MAM00914 3php C03232 HMDB0001024 CHEBI:30933 105 HC01082 3php MNXM541 O=C([O-])C(=O)COP(=O)([O-])[O-] InChI=1S/C3H5O7P/c4-2(3(5)6)1-10-11(7,8)9/h1H2,(H,5,6)(H2,7,8,9)/p-3 cpd02069 m00914c m00914c MAM00915c MAM00915 C03463 CHEBI:1359 M00915 MNXM39835 *[C@@H]1O[C@H](COP(=O)(O)O[C@H]2[C@@H](O)[C@H](*)O[C@@H]2COP(=O)(O)O[C@H]2[C@@H](O)[C@H](*)O[C@@H]2CO)[C@@H](OP(=O)(O)O)[C@H]1O cpd12325 m00915c m00915c MAM00916c MAM00916 pser__L C01005 HMDB0000272 CHEBI:15811 68841 HC00621 pser_L MNXM1094062 [NH3+][C@@H](COP(=O)([O-])[O-])C(=O)[O-] InChI=1S/C3H8NO6P/c4-2(3(5)6)1-10-11(7,8)9/h2H,1,4H2,(H,5,6)(H2,7,8,9)/p-2/t2-/m0/s1 cpd00738 m00916c m00916c -MAM00917c MAM00917 C19569 HMDB0000992 CHEBI:66942 437 M00917 MNXM97045 O=C(O)CCC(=O)c1cccnc1 InChI=1S/C9H9NO3/c11-8(3-4-9(12)13)7-2-1-5-10-6-7/h1-2,5-6H,3-4H2,(H,12,13) cpd20823 m00917c m00917c +MAM00917c MAM00917 C19569 HMDB0000992 CHEBI:66942 437 M00917 MNXM97045 O=C([O-])CCC(=O)c1cccnc1 InChI=1S/C9H9NO3/c11-8(3-4-9(12)13)7-2-1-5-10-6-7/h1-2,5-6H,3-4H2,(H,12,13)/p-1 cpd20823 m00917c m00917c MAM00918c MAM00918 3sala C00606 HMDB0000996 CHEBI:16345 28167170 HC00451 3sala MNXM1364516 N[C@@H](CS(=O)[O-])C(=O)[O-] InChI=1S/C3H7NO4S/c4-2(3(5)6)1-9(7)8/h2H,1,4H2,(H,5,6)(H,7,8)/p-2/t2-/m0/s1 cpd00467 m00918c m00918c MAM00918m MAM00918 3sala C00606 HMDB0000996 CHEBI:16345 28167170 HC00451 3sala MNXM1364516 N[C@@H](CS(=O)[O-])C(=O)[O-] InChI=1S/C3H7NO4S/c4-2(3(5)6)1-9(7)8/h2H,1,4H2,(H,5,6)(H,7,8)/p-2/t2-/m0/s1 cpd00467 m00918m m00918m MAM00919c MAM00919 3snpyr C05527 HMDB0001405 CHEBI:140699 110 3snpyr MNXM2484 O=C([O-])C(=O)CS(=O)[O-] InChI=1S/C3H4O5S/c4-2(3(5)6)1-9(7)8/h1H2,(H,5,6)(H,7,8)/p-2 cpd03284 m00919c m00919c From fd453e03745a2bb29ed954dfffc3aafa5ad62189 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:27:24 +0100 Subject: [PATCH 34/44] fix: test the two ordinary reactions that are filed under Pool reactions MAR01185 and MAR01227 convert one hydroxy-dodecenoate to (2E)-dodecenoyl-CoA, with a single substrate and product, so an elemental balance is defined for them, but the exclusion of the Pool reactions subsystem hid their charge imbalance. They are listed in ORDINARY_IN_LUMPED_SUBSYSTEMS and counted again. #1153 --- data/testResults/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 3585cf862..765093a5f 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -69,7 +69,7 @@ Metabolites with no charge, for the same reason as the formula check. #### Mass-imbalanced reactions Reactions whose elemental sums do not balance, from cobrapy's `check_mass_balance()`. Boundary reactions (exchange/demand/sink), biomass and the lumped pseudo-reactions are excluded, since an elemental balance is not defined for them: a lumped pseudo-reaction stands for a whole class of species at once, so its coefficients are an average over that class rather than a stoichiometry. -`balanceTest.py` recognises lumping two ways. Four subsystems consist of lumped reactions throughout, and are excluded wholesale (`LUMPED_SUBSYSTEMS`): `Pool reactions`, where a pool stands for the mixture of its members; `Artificial reactions`, where a conversion lumps a whole class of metabolites; and `Protein assembly` and `Protein degradation`, which translate and hydrolyse a named protein counted per amino-acid residue. The lumped reactions filed under an ordinary subsystem are listed by identifier instead, each with what it lumps (`LUMPED_REACTIONS`): five reactions that resolve a fatty-acid or cholesterol-ester pool into a weighted mixture of its members, and the five that polymerise and hydrolyse `DNA` and `RNA`, whose formulas are those of one average nucleotide. Every run audits that list and warns about an entry the model no longer needs, so it cannot quietly go stale. Subsystems are left as curated; the identifiers keep the exclusion in the test rather than relabelling reactions that users expect to find in their pathway. +`balanceTest.py` recognises lumping two ways. Four subsystems consist of lumped reactions throughout, and are excluded wholesale (`LUMPED_SUBSYSTEMS`): `Pool reactions`, where a pool stands for the mixture of its members; `Artificial reactions`, where a conversion lumps a whole class of metabolites; and `Protein assembly` and `Protein degradation`, which translate and hydrolyse a named protein counted per amino-acid residue. The lumped reactions filed under an ordinary subsystem are listed by identifier instead, each with what it lumps (`LUMPED_REACTIONS`): five reactions that resolve a fatty-acid or cholesterol-ester pool into a weighted mixture of its members, and the five that polymerise and hydrolyse `DNA` and `RNA`, whose formulas are those of one average nucleotide. Every run audits that list and warns about an entry the model no longer needs, so it cannot quietly go stale. Two ordinary reactions filed under `Pool reactions`, `MAR01185` and `MAR01227` (one hydroxy-dodecenoate to (2E)-dodecenoyl-CoA), are listed in `ORDINARY_IN_LUMPED_SUBSYSTEMS` and tested like any other reaction. Subsystems are left as curated; the identifiers keep the exclusion in the test rather than relabelling reactions that users expect to find in their pathway. `R` and `X` are treated as elements of their own rather than ignored, so a reaction using them is still expected to balance in them. Several do not, and that is a finding rather than noise. From 5ae4fbf4e8eacdd071d28119b99f532876a7713a Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:27:24 +0100 Subject: [PATCH 35/44] doc: restore the Zenodo registry row and describe the porphyrinogen review as the paper states it The row of 10.5281/zenodo.3583004 returns to its text on develop, and the row of 10.3390/biom16081188 states that the review gives no stoichiometry with O2 or H2O2, that oxidation also gives non-porphyrin products, and that other enzymes or processes account for a large part of the microsomal oxidation. #1153 --- literature/registry.md | 2 +- literature/registry.tsv | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/literature/registry.md b/literature/registry.md index 8c7430569..6f3c502ad 100644 --- a/literature/registry.md +++ b/literature/registry.md @@ -205,7 +205,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Siegel D et al. (1997). The Reduction of α-Tocopherolquinone by Human NAD(P)H:Quinone Oxidoreductase: The Role of α-Tocopherolhydroquinone as a Cellular Antioxidant. *Molecular Pharmacology*. [doi:10.1124/mol.52.2.300](https://doi.org/10.1124/mol.52.2.300) | Homo sapiens | NQO1 | `MAR03047` | Purified human NQO1 reduced alpha-tocopherolquinone to the hydroquinone (Km 370 uM, kcat 5.6e3 per min) and did so more efficiently than coenzyme Q10; in CHO cells expressing human NQO1 the hydroquinone formed correlated with NQO1 activity and protected against lipid peroxidation. Purified enzyme plus a hamster cell model; the abstract does not mention CBR1 (also in the GPR). | Abstract | enzyme assay, metabolite measurement | abstract | Human-GEM | | Simpson G et al. (2000). The non-oxidative degradation of ascorbic acid at physiological conditions. *Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease*. [doi:10.1016/s0925-4439(00)00009-0](https://doi.org/10.1016/s0925-4439(00)00009-0) | in vitro chemistry | | `MAR08625` | At pH 7.0 and 37 degrees C, L-erythrulose and oxalate were the main degradation products of ascorbate, dehydroascorbate and 2,3-diketogulonate, identified by 13C NMR and HPLC; the molar yield of erythrulose from 2,3-diketogulonate was high (about 97 percent given in the abstract). Chemistry in buffer, no enzyme involved, so it supports a spontaneous reaction only in vitro. | Abstract | metabolite measurement | abstract | Human-GEM#1173 | | Singh C et al. (2017). Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m116.760744](https://doi.org/10.1074/jbc.m116.760744), [PMID:27909055](https://pubmed.ncbi.nlm.nih.gov/27909055/) | Saccharomyces cerevisiae;Homo sapiens | FGGY | `MAR08726` | Ribulose changed most in a yeast YDR109C deletion, and FGGY silencing in HEK293 cells raised ribulose (seen only with ribitol added); recombinant yeast and human FGGY preferred D-ribulose over other sugars. The authors speculate a metabolite-repair role. | Abstract | enzyme assay, knockdown phenotype, metabolite measurement | abstract | Human-GEM#1171 | -| Smith AG (2026). Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences. *Biomolecules*. [doi:10.3390/biom16081188](https://doi.org/10.3390/biom16081188), [PMID:42650854](https://pubmed.ncbi.nlm.nih.gov/42650854/) | multiple | CYP1A2 | `MAR04768`, `MAR04769`, `MAR04770`, `MAR04773` | Review of the oxidation of porphyrinogens to porphyrins. Uroporphyrinogens and coproporphyrinogens oxidise to the porphyrins in air, with iron and with reactive oxygen species, without an enzyme, and the review treats this as the usual route. In mouse, Cyp1a2 knockout prevents experimental uroporphyria, and reconstituted mouse CYP1A2 oxidises uroporphyrinogen; the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; the CYP1A2 data are from mouse and rat, and it gives no CYP1A2 data for coproporphyrinogens | Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice | review, knockout phenotype | full text | Human-GEM#1153 | +| Smith AG (2026). Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences. *Biomolecules*. [doi:10.3390/biom16081188](https://doi.org/10.3390/biom16081188), [PMID:42650854](https://pubmed.ncbi.nlm.nih.gov/42650854/) | multiple | CYP1A2 | `MAR04768`, `MAR04769`, `MAR04770`, `MAR04773` | Review of the oxidation of porphyrinogens to porphyrins. Uroporphyrinogens, and in places coproporphyrinogens, are oxidised to the porphyrins in air, with iron and with reactive oxygen species; the review says the uroporphyrinogens are easily oxidised to the respective uroporphyrins, and that oxidation also gives non-porphyrin products such as chlorins. In mouse, Cyp1a2 knockout prevents experimental uroporphyria and reconstituted mouse CYP1A2 oxidises uroporphyrinogen, but the review also says that a large part of the microsomal oxidation is due to other enzymes or processes; the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; it gives no stoichiometry with O2 or H2O2 and no CYP1A2 data for coproporphyrinogens, and the CYP1A2 data are from mouse and rat | Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice | review, knockout phenotype | full text | Human-GEM#1153 | | Smith G et al. (2003). Cutaneous expression of cytochrome P450 CYP2S1: individuality in regulation by therapeutic agents for psoriasis and other skin diseases. *The Lancet*. [doi:10.1016/s0140-6736(03)13081-4](https://doi.org/10.1016/s0140-6736(03)13081-4) | Homo sapiens | CYP2S1 | `MAR06700`, `MAR06701` | RT-PCR in skin of 27 healthy volunteers and 29 psoriasis patients: CYP2S1 is expressed in skin with large individual variation and is induced by UV, PUVA, coal tar and all-trans retinoic acid. The abstract reports regulation of expression, not metabolism of retinoic acid by the enzyme; the claim that CYP2S1 metabolises retinoate is not stated in the abstract and the full text was not read. | Abstract | expression, clinical | abstract | Human-GEM#1169 | | Sontag T, Parker R (2002). Cytochrome P450 omega-Hydroxylase Pathway of Tocopherol Catabolism. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m201466200](https://doi.org/10.1074/jbc.m201466200) | Homo sapiens;Rattus norvegicus | CYP4F2 | | Tocopherols are catabolised by P450 omega-hydroxylation of the phytyl chain followed by stepwise chain shortening to the 3'-carboxychromanol; intermediates of gamma-tocopherol were identified by GC-MS in hepatocyte cultures, and among recombinant human P450s only CYP4F2 had omega-hydroxylase activity, with higher activity for gamma- than alpha-tocopherol. Rat and human liver microsomes and cultured hepatocytes. | Abstract | enzyme assay, metabolite measurement | abstract | Human-GEM#1118, Human-GEM#1163 | | Suetake I et al. (2004). DNMT3L Stimulates the DNA Methylation Activity of Dnmt3a and Dnmt3b through a Direct Interaction. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m400181200](https://doi.org/10.1074/jbc.m400181200), [PMID:15105426](https://pubmed.ncbi.nlm.nih.gov/15105426/) | Mus musculus | Dnmt3l, Dnmt3a, Dnmt3b | `MAR04072`, `MAR08640`, `MAR08641` | In vitro, human DNMT3L raised the DNA methylation activity of mouse Dnmt3a and Dnmt3b 1.5- to 3-fold, increasing with the DNMT3L amount, without affecting Dnmt1, and the effect held for all DNA substrates tested, including imprinted loci, a CpG island and synthetic polynucleotides. DNMT3L bound Dnmt3a and Dnmt3b but not DNA, and the C-terminal half carried the stimulatory effect, so the authors attribute it to a direct action on catalytic activity rather than DNA targeting. | Abstract | enzyme assay | abstract | Human-GEM#1155, animal-GEM | diff --git a/literature/registry.tsv b/literature/registry.tsv index 97c146ece..d2eed703b 100644 --- a/literature/registry.tsv +++ b/literature/registry.tsv @@ -178,7 +178,7 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1085/jgp.114.3.429 Lu CC, Hilgemann DW 1999 Gat1 (Gaba:Na+:Cl−) Cotransport Function The Journal of General Physiology Xenopus laevis (expression system) SLC6A1 MAR09613 Giant membrane patches from Xenopus oocytes expressing GAT1 gave reversal potentials consistent with a stoichiometry of 1 GABA : 2 Na+ : 1 Cl-. Expression-system study; the species of the GAT1 clone is not stated in the abstract. Abstract; Fig. 6 enzyme assay;expression full text Human-GEM#1173 10.1124/mol.58.6.1341 Marill J et al. 2000 Identification of Human Cytochrome P450s Involved in the Formation of All-trans-Retinoic Acid Principal Metabolites Molecular Pharmacology Homo sapiens CYP3A7;CYP3A5;CYP2C18;CYP2C8;CYP3A4;CYP2C9;CYP2B6;CYP2A6;CYP4A11;CYP1A1 MAR06700;MAR06701 Human liver microsomes and cDNA-expressed P450s formed 4-OH-RA and 4-oxo-RA mainly via CYP3A7, then CYP3A5, 2C8, 2C18, 3A4 and 2C9 (4-OH-RA by expressed P450s, ranked by Vmax/Km); CYP2B6 and 2A6 correlated with formation in liver microsomes. CYP26 enzymes and CYP2S1 are not among the P450s tested. Abstract enzyme assay;expression abstract Human-GEM#1169;Human-GEM#1118;Human-GEM#1163 10.1172/jci10902 Schwarz M et al. 2000 The bile acid synthetic gene 3β-hydroxy-Δ5-C27-steroid oxidoreductase is mutated in progressive intrahepatic cholestasis Journal of Clinical Investigation Homo sapiens;Mus musculus HSD3B7 MAR01796 Expression cloning gave a microsomal liver C27 3beta-HSD (HSD3B7) that acted on four 7alpha-hydroxylated sterols when transfected into cultured cells but not on C19/C21 steroids; a 2-bp deletion in HSD3B7 in a patient with neonatal cholestasis abolished activity. Cell-transfection assays; mouse used for mRNA regulation, human for the gene and the patient mutation. Abstract enzyme assay;clinical;expression abstract Human-GEM#1174 -10.5281/zenodo.3583004 Robinson JL et al. 2019 "Supplementary data and scripts for \""An Atlas of Human Metabolism\""" Zenodo Homo sapiens genome-wide Zenodo dataset (Human1_Publication_Data_Scripts.zip) with the models, data and scripts of the Human1 paper (tINIT GEMs, ecGEMs and others); the draft cites the script compare_gene_essentiality_results.m for the statement that Human1 predicted genes absent from a context model as non-essential. The script was not opened here, so that statement is taken from the draft. Zenodo record description model secondary Human-GEM#1175 +10.5281/zenodo.3583004 Robinson JL et al. 2019 Supplementary data and scripts for \"An Atlas of Human Metabolism\" Zenodo Homo sapiens genome-wide Zenodo dataset (Human1_Publication_Data_Scripts.zip) with the models, data and scripts of the Human1 paper (tINIT GEMs, ecGEMs and others); the draft cites the script compare_gene_essentiality_results.m for the statement that Human1 predicted genes absent from a context model as non-essential. The script was not opened here, so that statement is taken from the draft. Zenodo record description model secondary Human-GEM#1175 10.1007/bf03226377 Banoglu E et al. 2001 Hepatic microsomal metabolism of indole to indoxyl, a precursor of indoxyl sulfate European Journal of Drug Metabolism and Pharmacokinetics Rattus norvegicus CYP2E1 MAR10461 Rat liver microsomes with an NADPH-generating system oxidised indole to indoxyl (measured as indigo) with apparent Km 0.85 mM; inhibitor and inducer experiments showed P450 rather than FMO activity, and activity tracked CYP2E1 activity, so the authors conclude CYP2E1 is the major isoform. Rat microsomes only, no human enzyme tested. Abstract enzyme assay abstract Human-GEM#1173 10.1016/j.abb.2006.04.013 Fraisl P et al. 2006 A novel mammalian bubblegum-related acyl-CoA synthetase restricted to testes and possibly involved in spermatogenesis Archives of Biochemistry and Biophysics Homo sapiens; Mus musculus ACSBG2 MAR00249;MAR02957 A newly characterised membrane-associated acyl-CoA synthetase (BGR, ACSBG2) showed activity on long- and very long-chain fatty acids; its human mRNA was detected only in testis, and mouse Bgr was found in testis germ and Sertoli cells. The abstract does not name stearate, so it does not show activity on that substrate. Abstract enzyme assay;expression abstract Human-GEM#1169 10.1016/j.jpba.2012.02.002 de los Ángeles Juricic M et al. 2012 Salsolinol and isosalsolinol: Condensation products of acetaldehyde and dopamine. Separation of their enantiomers in the presence of a large excess of dopamine Journal of Pharmaceutical and Biomedical Analysis in vitro MAR06734;MAR06738 An analytical methods paper: HPLC, NMR and MS showed commercial salsolinol contains about 10% isosalsolinol, and an HPLC method separates the (S)- and (R)-salsolinol enantiomers in the presence of excess dopamine. The condensation of dopamine with acetaldehyde in vitro, the pyruvate route and a putative (R)-salsolinol synthase are stated only as background (suggested or postulated), not shown. Abstract; Introduction (background statements) metabolite measurement full text Human-GEM#1173 @@ -239,4 +239,4 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1016/0003-9861(89)90112-4 2916844 Leo MA et al. 1989 Metabolism of retinol and retinoic acid by human liver cytochrome P450IIC8 Archives of Biochemistry and Biophysics Homo sapiens CYP2C8 MAR06634 Human liver microsomes from nine subjects, and a reconstituted system with purified CYP2C8, NADPH and P450 reductase, converted retinol to 4-hydroxyretinol and other polar metabolites that were not identified (Km 0.071 mM, Vmax 1.73 nmol per min per nmol P450); purified CYP2C9 and CYP2E1 had no significant retinol hydroxylase activity, and an antibody against CYP2C8 inhibited the reaction in microsomes. The CYP2C8 system also converted retinoic acid to polar products that include 4-hydroxy- and 4-oxoretinoic acid. 4-Oxoretinol is not reported as a product of retinol. Limits: in vitro; the other polar products were not identified; CYP26A1 was not tested Abstract; Results (Table I, Fig. 1); the retinoic acid paragraph of the Results enzyme assay full text Human-GEM#1153 10.1016/j.abb.2004.07.002 15369820 Martras S et al. 2004 Kinetics of human alcohol dehydrogenase with ring-oxidized retinoids: effect of Tween 80 Archives of Biochemistry and Biophysics Homo sapiens ADH1B;ADH4 MAR20067;MAR20068 Recombinant human ADH1B1, ADH1B2 and ADH4 acted on 4-hydroxyretinol with NAD+ (retinol oxidation assay) and on 4-oxoretinal with NADH (retinal reduction assay) at the highest rates of any retinoid tested (ADH4 kcat 2050 per min with 4-hydroxyretinol, a 3- to 40-fold increase over retinol and retinal). The authors state that the conversion of 4-hydroxyretinol and 4-oxoretinol to the corresponding retinoic acids has not been documented, and that oxidation of the ring of retinoic acid by P450s is well demonstrated. The paper does not show the oxidation of the ring 4-hydroxyl of 4-hydroxyretinol to 4-oxoretinol. Limits: in vitro with Tween 80, which inhibits competitively and raises Km about 10-fold Abstract; Results (Table 1); Discussion enzyme assay full text Human-GEM#1153 10.1021/tx980005y 9625726 Hecht SS 1998 Biochemistry, Biology, and Carcinogenicity of Tobacco-Specific N-Nitrosamines Chemical Research in Toxicology multiple MAR07070;MAR07076 Review of the metabolism of the tobacco-specific nitrosamines. It states that keto acid is formed in vivo from keto alcohol (HPB) in rats and in some in vitro systems (cultured rat oral tissue and esophagus), that keto acid is also a likely oxidation product of keto aldehyde although this does not seem to have been investigated, and that hydroxy acid arises from NNAL by further oxidation of the lactol and the diol and not by reduction of keto acid. It names no enzyme or cofactor for these oxidations. Limits: a review that cites the underlying studies; the rat data are cited from other work Sections 2.1.1.4 (alpha-methyl hydroxylation) and 2.1.3.3 (alpha-hydroxylation) review full text Human-GEM#1153 -10.3390/biom16081188 42650854 Smith AG 2026 Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences Biomolecules multiple CYP1A2 MAR04768;MAR04769;MAR04770;MAR04773 Review of the oxidation of porphyrinogens to porphyrins. Uroporphyrinogens and coproporphyrinogens oxidise to the porphyrins in air, with iron and with reactive oxygen species, without an enzyme, and the review treats this as the usual route. In mouse, Cyp1a2 knockout prevents experimental uroporphyria, and reconstituted mouse CYP1A2 oxidises uroporphyrinogen; the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; the CYP1A2 data are from mouse and rat, and it gives no CYP1A2 data for coproporphyrinogens Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice review;knockout phenotype full text Human-GEM#1153 +10.3390/biom16081188 42650854 Smith AG 2026 Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences Biomolecules multiple CYP1A2 MAR04768;MAR04769;MAR04770;MAR04773 Review of the oxidation of porphyrinogens to porphyrins. Uroporphyrinogens, and in places coproporphyrinogens, are oxidised to the porphyrins in air, with iron and with reactive oxygen species; the review says the uroporphyrinogens are easily oxidised to the respective uroporphyrins, and that oxidation also gives non-porphyrin products such as chlorins. In mouse, Cyp1a2 knockout prevents experimental uroporphyria and reconstituted mouse CYP1A2 oxidises uroporphyrinogen, but the review also says that a large part of the microsomal oxidation is due to other enzymes or processes; the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; it gives no stoichiometry with O2 or H2O2 and no CYP1A2 data for coproporphyrinogens, and the CYP1A2 data are from mouse and rat Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice review;knockout phenotype full text Human-GEM#1153 From 1edb25ecafbc87f08789a0b0c241b6948fd3fa7d Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:37:40 +0100 Subject: [PATCH 36/44] fix: the 1-(1-alkenyl)-sn-glycerol 3-phosphate is the dianion, as the 1-alkyl analogue MAM00222 was written as the neutral phosphoric acid (charge 0) while the 1-alkyl-sn-glycerol 3-phosphate and the 2-acyl-1-(1-alkenyl)-sn-glycerol 3-phosphate are dianions (charge -2). It is now C3H4O6PR with charge -2, and MAR07607 releases a proton instead of taking one. The change follows data/modelCuration/alkenylGlycerolPhosphateProtonation.tsv (applyCurationTable.py). #1153 --- data/modelCuration/README.md | 1 + data/modelCuration/alkenylGlycerolPhosphateProtonation.tsv | 5 +++++ model/Human-GEM.yml | 6 +++--- model/metabolites.tsv | 2 +- 4 files changed, 10 insertions(+), 4 deletions(-) create mode 100644 data/modelCuration/alkenylGlycerolPhosphateProtonation.tsv diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index 326e0f783..c0b3cc1b4 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -63,3 +63,4 @@ Static dumps of external sources that were kept here during the Human1 series (S - `aflatoxinDialcoholProtonation.tsv`: per-entity table of the change "the aflatoxin B1 dialcohol is the phenolate, like the dialdehyde and the monoalcohols, and its two reductions take one proton" (`code/modelCuration/applyCurationTable.py`). - `aflatoxinPhenolateStructures.tsv`: per-entity table of the change "the SMILES and InChI of the aflatoxin B1 dialdehyde and the two monoalcohols are the phenolate" (`code/modelCuration/applyCurationTable.py`). - `succinoylpyridineProtonation.tsv`: per-entity table of the change "3-succinoylpyridine is the carboxylate, as the hydroxy acid formed in parallel, and its two formation reactions follow" (`code/modelCuration/applyCurationTable.py`). +- `alkenylGlycerolPhosphateProtonation.tsv`: per-entity table of the change "the 1-(1-alkenyl)-sn-glycerol 3-phosphate is the phosphate dianion, like the 1-alkyl-sn-glycerol 3-phosphate, and its release from the glycerophosphoethanolamine follows" (`code/modelCuration/applyCurationTable.py`). diff --git a/data/modelCuration/alkenylGlycerolPhosphateProtonation.tsv b/data/modelCuration/alkenylGlycerolPhosphateProtonation.tsv new file mode 100644 index 000000000..93a7adbc4 --- /dev/null +++ b/data/modelCuration/alkenylGlycerolPhosphateProtonation.tsv @@ -0,0 +1,5 @@ +entity field before after +MAM00222c formula C3H6O6PR C3H4O6PR +MAM00222c charge 0 -2 +MAM00222c metSmiles */C=C\OC[C@@H](O)COP(=O)(O)O */C=C\OC[C@@H](O)COP(=O)([O-])[O-] +MAR07607 metabolites MAM00222c:1.0;MAM00223c:-1.0;MAM01797c:1.0;MAM02039c:-1.0;MAM02040c:-1.0 MAM00222c:1.0;MAM00223c:-1.0;MAM01797c:1.0;MAM02039c:1.0;MAM02040c:-1.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 626796031..d3502aff5 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -2971,8 +2971,8 @@ - id: MAM00222c - name: 1-(1-alkenyl)-sn-glycero-3-phosphate - compartment: c - - charge: 0.0 - - formula: C3H6O6PR + - charge: -2.0 + - formula: C3H4O6PR - metFrom: HMRdatabase - !!omap - id: MAM00223c @@ -129588,7 +129588,7 @@ - MAM00222c: 1.0 - MAM00223c: -1.0 - MAM01797c: 1.0 - - MAM02039c: -1.0 + - MAM02039c: 1.0 - MAM02040c: -1.0 - lower_bound: 0.0 - upper_bound: 1000.0 diff --git a/model/metabolites.tsv b/model/metabolites.tsv index 544fda5e0..7b2374b14 100644 --- a/model/metabolites.tsv +++ b/model/metabolites.tsv @@ -419,7 +419,7 @@ MAM00217c MAM00217 C03721 M00217 MNXM93873 *NC(=O)[C@H](Cc1ccc(OS(=O)(=O) MAM00219c MAM00219 C01256 M00219 MNXM96103 *NC(=O)[C@H](CO)NC(*)=O cpd11834 m00219c m00219c MAM00220c MAM00220 C01293 M00220 MNXM92072 *NC(=O)[C@H](COP(=O)(O)O)NC(*)=O cpd11840 m00220c m00220c MAM00221c MAM00221 CE3140 HMDB0012492 CHEBI:169367 21125948 CE3140 CE3140 MNXM32416 O=C(O)C1Cc2c([nH]c3ccccc23)C(C(O)C(O)C(O)C(O)CO)N1 InChI=1S/C17H22N2O7/c20-6-11(21)14(22)16(24)15(23)13-12-8(5-10(19-13)17(25)26)7-3-1-2-4-9(7)18-12/h1-4,10-11,13-16,18-24H,5-6H2,(H,25,26) m00221c m00221c -MAM00222c MAM00222 C15646 M00222 MNXM91814 */C=C\OC[C@@H](O)COP(=O)(O)O cpd14505 m00222c m00222c +MAM00222c MAM00222 C15646 M00222 MNXM91814 */C=C\OC[C@@H](O)COP(=O)([O-])[O-] cpd14505 m00222c m00222c MAM00223c MAM00223 C04635 CHEBI:15785 M00223 MNXM162356 *C=COC[C@H](O)COP(=O)(O)OCCN cpd02822 m00223c m00223c MAM00224c MAM00224 C15645 M00224 MNXM164025 */C=C\OC[C@@H](O)CO cpd14504 m00224c m00224c MAM00225c MAM00225 C19582 HMDB0062266 CHEBI:82576 156653 M00225 MNXM9553 OCCCC(O)c1cccnc1 InChI=1S/C9H13NO2/c11-6-2-4-9(12)8-3-1-5-10-7-8/h1,3,5,7,9,11-12H,2,4,6H2 cpd20836 m00225c m00225c From 699db40b75fa3e1daa67cea9843c3c327ac5b940 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:37:44 +0100 Subject: [PATCH 37/44] fix: MAR07070 and MAR07076 do not cite the NNK study of human lung microsomes PMID:7585636 reports the formation of the keto acid from NNK in human lung microsomes without NADPH. It does not show the conversion of the keto alcohol to the keto acid or of the diol to the hydroxy acid, so it is not a reference of these two reactions. The change follows data/modelCuration/nnkOxidationsWithoutCofactor.tsv (applyCurationTable.py). #1153 --- data/modelCuration/nnkOxidationsWithoutCofactor.tsv | 2 -- model/Human-GEM.yml | 4 ++-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/data/modelCuration/nnkOxidationsWithoutCofactor.tsv b/data/modelCuration/nnkOxidationsWithoutCofactor.tsv index 83c380880..3882c6c59 100644 --- a/data/modelCuration/nnkOxidationsWithoutCofactor.tsv +++ b/data/modelCuration/nnkOxidationsWithoutCofactor.tsv @@ -4,6 +4,4 @@ MAR07070 metabolites MAM00917c:1.0;MAM00985c:-1.0;MAM02039c:1.0;MAM02040c:1.0;MA MAR07076 name 1-(3-pyridinyl)-1,4-butanediol hydroxylation 1-(3-pyridinyl)-1,4-butanediol oxidation MAR07076 metabolites MAM00225c:-1.0;MAM01929c:1.0;MAM02039c:2.0;MAM02040c:1.0;MAM02554c:1.0;MAM02555c:-1.0;MAM02630c:-1.0 MAM00225c:-1.0;MAM01929c:1.0;MAM02039c:1.0;MAM02040c:1.0;MAM02630c:-1.0 MAR07070 references doi:10.1021/tx980005y -MAR07070 references doi:10.1021/tx980005y doi:10.1021/tx980005y;PMID:7585636 MAR07076 references doi:10.1021/tx980005y -MAR07076 references doi:10.1021/tx980005y doi:10.1021/tx980005y;PMID:7585636 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index d3502aff5..6d8d5b881 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -149831,7 +149831,7 @@ - upper_bound: 1000.0 - subsystem: - Xenobiotics metabolism - - references: doi:10.1021/tx980005y;PMID:7585636 + - references: doi:10.1021/tx980005y - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap @@ -149918,7 +149918,7 @@ - upper_bound: 1000.0 - subsystem: - Xenobiotics metabolism - - references: doi:10.1021/tx980005y;PMID:7585636 + - references: doi:10.1021/tx980005y - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap From 04288f7ae4cba57bcf8fd8ad58c76710e2ed67ac Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:37:54 +0100 Subject: [PATCH 38/44] doc: registry row of the porphyrinogen review states the knockout caveats as the paper does #1153 --- literature/registry.md | 2 +- literature/registry.tsv | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/literature/registry.md b/literature/registry.md index 6f3c502ad..aa9d0a74e 100644 --- a/literature/registry.md +++ b/literature/registry.md @@ -205,7 +205,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Siegel D et al. (1997). The Reduction of α-Tocopherolquinone by Human NAD(P)H:Quinone Oxidoreductase: The Role of α-Tocopherolhydroquinone as a Cellular Antioxidant. *Molecular Pharmacology*. [doi:10.1124/mol.52.2.300](https://doi.org/10.1124/mol.52.2.300) | Homo sapiens | NQO1 | `MAR03047` | Purified human NQO1 reduced alpha-tocopherolquinone to the hydroquinone (Km 370 uM, kcat 5.6e3 per min) and did so more efficiently than coenzyme Q10; in CHO cells expressing human NQO1 the hydroquinone formed correlated with NQO1 activity and protected against lipid peroxidation. Purified enzyme plus a hamster cell model; the abstract does not mention CBR1 (also in the GPR). | Abstract | enzyme assay, metabolite measurement | abstract | Human-GEM | | Simpson G et al. (2000). The non-oxidative degradation of ascorbic acid at physiological conditions. *Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease*. [doi:10.1016/s0925-4439(00)00009-0](https://doi.org/10.1016/s0925-4439(00)00009-0) | in vitro chemistry | | `MAR08625` | At pH 7.0 and 37 degrees C, L-erythrulose and oxalate were the main degradation products of ascorbate, dehydroascorbate and 2,3-diketogulonate, identified by 13C NMR and HPLC; the molar yield of erythrulose from 2,3-diketogulonate was high (about 97 percent given in the abstract). Chemistry in buffer, no enzyme involved, so it supports a spontaneous reaction only in vitro. | Abstract | metabolite measurement | abstract | Human-GEM#1173 | | Singh C et al. (2017). Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m116.760744](https://doi.org/10.1074/jbc.m116.760744), [PMID:27909055](https://pubmed.ncbi.nlm.nih.gov/27909055/) | Saccharomyces cerevisiae;Homo sapiens | FGGY | `MAR08726` | Ribulose changed most in a yeast YDR109C deletion, and FGGY silencing in HEK293 cells raised ribulose (seen only with ribitol added); recombinant yeast and human FGGY preferred D-ribulose over other sugars. The authors speculate a metabolite-repair role. | Abstract | enzyme assay, knockdown phenotype, metabolite measurement | abstract | Human-GEM#1171 | -| Smith AG (2026). Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences. *Biomolecules*. [doi:10.3390/biom16081188](https://doi.org/10.3390/biom16081188), [PMID:42650854](https://pubmed.ncbi.nlm.nih.gov/42650854/) | multiple | CYP1A2 | `MAR04768`, `MAR04769`, `MAR04770`, `MAR04773` | Review of the oxidation of porphyrinogens to porphyrins. Uroporphyrinogens, and in places coproporphyrinogens, are oxidised to the porphyrins in air, with iron and with reactive oxygen species; the review says the uroporphyrinogens are easily oxidised to the respective uroporphyrins, and that oxidation also gives non-porphyrin products such as chlorins. In mouse, Cyp1a2 knockout prevents experimental uroporphyria and reconstituted mouse CYP1A2 oxidises uroporphyrinogen, but the review also says that a large part of the microsomal oxidation is due to other enzymes or processes; the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; it gives no stoichiometry with O2 or H2O2 and no CYP1A2 data for coproporphyrinogens, and the CYP1A2 data are from mouse and rat | Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice | review, knockout phenotype | full text | Human-GEM#1153 | +| Smith AG (2026). Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences. *Biomolecules*. [doi:10.3390/biom16081188](https://doi.org/10.3390/biom16081188), [PMID:42650854](https://pubmed.ncbi.nlm.nih.gov/42650854/) | multiple | CYP1A2 | `MAR04768`, `MAR04769`, `MAR04770`, `MAR04773` | Review of the oxidation of porphyrinogens to porphyrins. The review says the uroporphyrinogens are easily oxidised to the respective uroporphyrins in air, with iron and with reactive oxygen species, and that oxidation also gives non-porphyrin products such as chlorins. In mouse, Cyp1a2 knockout prevents experimental uroporphyria under the conditions reported, although uroporphyria is ultimately possible in Cyp1a2 knockout mice and Cyp1a1 knockout mice are also protected; the review says an appreciable proportion of the microsomal oxidation seems due to other CYP enzymes or processes. Reconstituted mouse CYP1A2 oxidises uroporphyrinogen, the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; it gives no stoichiometry with O2 or H2O2 and no CYP1A2 data for coproporphyrinogens, and the CYP1A2 data are from mouse and rat | Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice | review, knockout phenotype | full text | Human-GEM#1153 | | Smith G et al. (2003). Cutaneous expression of cytochrome P450 CYP2S1: individuality in regulation by therapeutic agents for psoriasis and other skin diseases. *The Lancet*. [doi:10.1016/s0140-6736(03)13081-4](https://doi.org/10.1016/s0140-6736(03)13081-4) | Homo sapiens | CYP2S1 | `MAR06700`, `MAR06701` | RT-PCR in skin of 27 healthy volunteers and 29 psoriasis patients: CYP2S1 is expressed in skin with large individual variation and is induced by UV, PUVA, coal tar and all-trans retinoic acid. The abstract reports regulation of expression, not metabolism of retinoic acid by the enzyme; the claim that CYP2S1 metabolises retinoate is not stated in the abstract and the full text was not read. | Abstract | expression, clinical | abstract | Human-GEM#1169 | | Sontag T, Parker R (2002). Cytochrome P450 omega-Hydroxylase Pathway of Tocopherol Catabolism. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m201466200](https://doi.org/10.1074/jbc.m201466200) | Homo sapiens;Rattus norvegicus | CYP4F2 | | Tocopherols are catabolised by P450 omega-hydroxylation of the phytyl chain followed by stepwise chain shortening to the 3'-carboxychromanol; intermediates of gamma-tocopherol were identified by GC-MS in hepatocyte cultures, and among recombinant human P450s only CYP4F2 had omega-hydroxylase activity, with higher activity for gamma- than alpha-tocopherol. Rat and human liver microsomes and cultured hepatocytes. | Abstract | enzyme assay, metabolite measurement | abstract | Human-GEM#1118, Human-GEM#1163 | | Suetake I et al. (2004). DNMT3L Stimulates the DNA Methylation Activity of Dnmt3a and Dnmt3b through a Direct Interaction. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m400181200](https://doi.org/10.1074/jbc.m400181200), [PMID:15105426](https://pubmed.ncbi.nlm.nih.gov/15105426/) | Mus musculus | Dnmt3l, Dnmt3a, Dnmt3b | `MAR04072`, `MAR08640`, `MAR08641` | In vitro, human DNMT3L raised the DNA methylation activity of mouse Dnmt3a and Dnmt3b 1.5- to 3-fold, increasing with the DNMT3L amount, without affecting Dnmt1, and the effect held for all DNA substrates tested, including imprinted loci, a CpG island and synthetic polynucleotides. DNMT3L bound Dnmt3a and Dnmt3b but not DNA, and the C-terminal half carried the stimulatory effect, so the authors attribute it to a direct action on catalytic activity rather than DNA targeting. | Abstract | enzyme assay | abstract | Human-GEM#1155, animal-GEM | diff --git a/literature/registry.tsv b/literature/registry.tsv index d2eed703b..dc35701ed 100644 --- a/literature/registry.tsv +++ b/literature/registry.tsv @@ -239,4 +239,4 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1016/0003-9861(89)90112-4 2916844 Leo MA et al. 1989 Metabolism of retinol and retinoic acid by human liver cytochrome P450IIC8 Archives of Biochemistry and Biophysics Homo sapiens CYP2C8 MAR06634 Human liver microsomes from nine subjects, and a reconstituted system with purified CYP2C8, NADPH and P450 reductase, converted retinol to 4-hydroxyretinol and other polar metabolites that were not identified (Km 0.071 mM, Vmax 1.73 nmol per min per nmol P450); purified CYP2C9 and CYP2E1 had no significant retinol hydroxylase activity, and an antibody against CYP2C8 inhibited the reaction in microsomes. The CYP2C8 system also converted retinoic acid to polar products that include 4-hydroxy- and 4-oxoretinoic acid. 4-Oxoretinol is not reported as a product of retinol. Limits: in vitro; the other polar products were not identified; CYP26A1 was not tested Abstract; Results (Table I, Fig. 1); the retinoic acid paragraph of the Results enzyme assay full text Human-GEM#1153 10.1016/j.abb.2004.07.002 15369820 Martras S et al. 2004 Kinetics of human alcohol dehydrogenase with ring-oxidized retinoids: effect of Tween 80 Archives of Biochemistry and Biophysics Homo sapiens ADH1B;ADH4 MAR20067;MAR20068 Recombinant human ADH1B1, ADH1B2 and ADH4 acted on 4-hydroxyretinol with NAD+ (retinol oxidation assay) and on 4-oxoretinal with NADH (retinal reduction assay) at the highest rates of any retinoid tested (ADH4 kcat 2050 per min with 4-hydroxyretinol, a 3- to 40-fold increase over retinol and retinal). The authors state that the conversion of 4-hydroxyretinol and 4-oxoretinol to the corresponding retinoic acids has not been documented, and that oxidation of the ring of retinoic acid by P450s is well demonstrated. The paper does not show the oxidation of the ring 4-hydroxyl of 4-hydroxyretinol to 4-oxoretinol. Limits: in vitro with Tween 80, which inhibits competitively and raises Km about 10-fold Abstract; Results (Table 1); Discussion enzyme assay full text Human-GEM#1153 10.1021/tx980005y 9625726 Hecht SS 1998 Biochemistry, Biology, and Carcinogenicity of Tobacco-Specific N-Nitrosamines Chemical Research in Toxicology multiple MAR07070;MAR07076 Review of the metabolism of the tobacco-specific nitrosamines. It states that keto acid is formed in vivo from keto alcohol (HPB) in rats and in some in vitro systems (cultured rat oral tissue and esophagus), that keto acid is also a likely oxidation product of keto aldehyde although this does not seem to have been investigated, and that hydroxy acid arises from NNAL by further oxidation of the lactol and the diol and not by reduction of keto acid. It names no enzyme or cofactor for these oxidations. Limits: a review that cites the underlying studies; the rat data are cited from other work Sections 2.1.1.4 (alpha-methyl hydroxylation) and 2.1.3.3 (alpha-hydroxylation) review full text Human-GEM#1153 -10.3390/biom16081188 42650854 Smith AG 2026 Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences Biomolecules multiple CYP1A2 MAR04768;MAR04769;MAR04770;MAR04773 Review of the oxidation of porphyrinogens to porphyrins. Uroporphyrinogens, and in places coproporphyrinogens, are oxidised to the porphyrins in air, with iron and with reactive oxygen species; the review says the uroporphyrinogens are easily oxidised to the respective uroporphyrins, and that oxidation also gives non-porphyrin products such as chlorins. In mouse, Cyp1a2 knockout prevents experimental uroporphyria and reconstituted mouse CYP1A2 oxidises uroporphyrinogen, but the review also says that a large part of the microsomal oxidation is due to other enzymes or processes; the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; it gives no stoichiometry with O2 or H2O2 and no CYP1A2 data for coproporphyrinogens, and the CYP1A2 data are from mouse and rat Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice review;knockout phenotype full text Human-GEM#1153 +10.3390/biom16081188 42650854 Smith AG 2026 Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences Biomolecules multiple CYP1A2 MAR04768;MAR04769;MAR04770;MAR04773 Review of the oxidation of porphyrinogens to porphyrins. The review says the uroporphyrinogens are easily oxidised to the respective uroporphyrins in air, with iron and with reactive oxygen species, and that oxidation also gives non-porphyrin products such as chlorins. In mouse, Cyp1a2 knockout prevents experimental uroporphyria under the conditions reported, although uroporphyria is ultimately possible in Cyp1a2 knockout mice and Cyp1a1 knockout mice are also protected; the review says an appreciable proportion of the microsomal oxidation seems due to other CYP enzymes or processes. Reconstituted mouse CYP1A2 oxidises uroporphyrinogen, the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; it gives no stoichiometry with O2 or H2O2 and no CYP1A2 data for coproporphyrinogens, and the CYP1A2 data are from mouse and rat Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice review;knockout phenotype full text Human-GEM#1153 From 0a1e741ac00dc1ebc59051994ae822bd7e6aaa37 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:44:57 +0100 Subject: [PATCH 39/44] fix: balance MAR04769 as the oxidation of uroporphyrinogen I MAR04769 took uroporphyrin I to uroporphyrinogen III with six protons, which does not balance and joins two isomers; uroporphyrinogen I does not isomerise to the III isomer. It is now uroporphyrinogen I + 3 O2 => uroporphyrin I + 3 H2O2 in one direction, like the other porphyrinogen oxidations, and has no gene. KEGG R04971 has the same oxidation of uroporphyrinogen I to uroporphyrin I with an unspecified acceptor. The change follows data/modelCuration/porphyrinogenOxidation.tsv (applyCurationTable.py). #1153 --- data/modelCuration/porphyrinogenOxidation.tsv | 4 ++++ model/Human-GEM.yml | 13 +++++++------ 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/data/modelCuration/porphyrinogenOxidation.tsv b/data/modelCuration/porphyrinogenOxidation.tsv index f8949cc8a..e17bae4a5 100644 --- a/data/modelCuration/porphyrinogenOxidation.tsv +++ b/data/modelCuration/porphyrinogenOxidation.tsv @@ -12,3 +12,7 @@ MAR04773 name coproporphyrin I to coproporphyrinogen I conversion coproporphyrin MAR04773 metabolites MAM01603c:-1.0;MAM01605c:1.0;MAM02039c:-6.0 MAM01603c:1.0;MAM01605c:-1.0;MAM02041c:3.0;MAM02630c:-3.0 MAR04773 lower_bound -1000.0 0.0 MAR04773 references PMID:11281297 PMID:11281297;doi:10.3390/biom16081188 +MAR04769 name uroporphyrin I to uroporphyrinogen III conversion uroporphyrinogen I oxidation to uroporphyrin I +MAR04769 metabolites MAM02039c:-6.0;MAM03125c:-1.0;MAM03128c:1.0 MAM02041c:3.0;MAM02630c:-3.0;MAM03125c:1.0;MAM03127c:-1.0 +MAR04769 lower_bound -1000.0 0.0 +MAR04769 references PMID:11281297 PMID:11281297;doi:10.3390/biom16081188 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 6d8d5b881..0e2200bcf 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -144527,16 +144527,17 @@ - confidence_score: 0.0 - !!omap - id: MAR04769 - - name: uroporphyrin I to uroporphyrinogen III conversion + - name: uroporphyrinogen I oxidation to uroporphyrin I - metabolites: !!omap - - MAM02039c: -6.0 - - MAM03125c: -1.0 - - MAM03128c: 1.0 - - lower_bound: -1000.0 + - MAM02041c: 3.0 + - MAM02630c: -3.0 + - MAM03125c: 1.0 + - MAM03127c: -1.0 + - lower_bound: 0.0 - upper_bound: 1000.0 - subsystem: - Porphyrin metabolism - - references: PMID:11281297 + - references: PMID:11281297;doi:10.3390/biom16081188 - rxnFrom: HMRdatabase - confidence_score: 0.0 - !!omap From b24cee4b6c83e2c83126e0132c123cca45493a95 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:45:12 +0100 Subject: [PATCH 40/44] fix: remove MAR02023, the lumped nitric oxide synthase reaction MAR02023 (Recon3D r0145) is the sum of 2 MAR04190 (L-arginine to N-omega-hydroxyarginine) and MAR03993 (N-omega-hydroxyarginine to citrulline and nitric oxide): 2 L-arginine + H+ + 3 NADPH + 4 O2 => 2 citrulline + 2 NO + 3 NADP+ + 4 H2O. Both steps carry the same genes (NOS1, NOS2, NOS3) and EC number 1.14.13.39, so the lump only adds a bypass of the intermediate. The identifiers r0145 and MNXR163339 describe the lumped equation and stay in the deprecated list. #1153 --- .../deprecatedReactions.tsv | 1 + data/modelCuration/README.md | 1 - .../nitricOxideSynthaseStoichiometry.tsv | 2 -- model/Human-GEM.yml | 23 ------------------- model/reactions.tsv | 1 - 5 files changed, 1 insertion(+), 27 deletions(-) delete mode 100644 data/modelCuration/nitricOxideSynthaseStoichiometry.tsv diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 67c39ee8e..b246589ae 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -643,3 +643,4 @@ MAR04702 R02518 HMR_4702 HMR_4702 MNXR107561 rxn01824 HMR_4702 RCR11362 0 MAR04703 R02655 r0558 R02655C r0558 r0558 MNXR105348 rxn01918 HMR_4703 RCR11363 0 HMR_4703 MAR04704 R02657 r0559 R02657C r0559 r0559 MNXR105349 rxn01920 HMR_4704 RCR11364 0 HMR_4704 MAR02818 RE1519X;FAOXC101C102x RE1519X;FAOXC101C102x 0 RE1519X;FAOXC101C102x;MAR04966 +MAR02023 r0145 r0145 MNXR163339 0 r0145 diff --git a/data/modelCuration/README.md b/data/modelCuration/README.md index c0b3cc1b4..e7982bedc 100644 --- a/data/modelCuration/README.md +++ b/data/modelCuration/README.md @@ -48,7 +48,6 @@ This directory contains curation-related data files that support changes to the Static dumps of external sources that were kept here during the Human1 series (SwissProt / Cell Atlas / DeepLoc2 subcellular locations, Rhea reaction associations, and metabolite SMILES/InChI) have been removed for the Human2 release. They had gone stale and are better queried fresh from the source when needed. They remain in the git history and in the last Human1 release, [v1.19.0](https://github.com/SysBioChalmers/Human-GEM/releases/tag/v1.19.0). - `aflatoxinDialdehydeReductions.tsv`: per-entity table of the change "aflatoxin B1 dialdehyde reductions take NADPH" (`code/modelCuration/applyCurationTable.py`). - `dibenzoPyreneDiolEpoxide.tsv`: per-entity table of the change "formula of the dibenzo[a,l]pyrene diol epoxide and the proton of its formation" (`code/modelCuration/applyCurationTable.py`). -- `nitricOxideSynthaseStoichiometry.tsv`: per-entity table of the change "stoichiometry of the arginine nitric oxide synthase reaction" (`code/modelCuration/applyCurationTable.py`). - `alkenylEtherLipidFormulas.tsv`: per-entity table of the change "the vinyl ether carbons of the alkenyl ether lipids are counted inside R" (`code/modelCuration/applyCurationTable.py`). - `steroidDeltaIsomerase.tsv`: per-entity table of the change "the Delta-isomerase of androstenedione has no cofactor" (`code/modelCuration/applyCurationTable.py`). - `catecholEstrogenPeroxidase.tsv`: per-entity table of the change "the peroxidases oxidise two catechol estrogens per H2O2" (`code/modelCuration/applyCurationTable.py`). diff --git a/data/modelCuration/nitricOxideSynthaseStoichiometry.tsv b/data/modelCuration/nitricOxideSynthaseStoichiometry.tsv deleted file mode 100644 index a4ba8cd93..000000000 --- a/data/modelCuration/nitricOxideSynthaseStoichiometry.tsv +++ /dev/null @@ -1,2 +0,0 @@ -entity field before after -MAR02023 metabolites MAM01365c:-1.0;MAM01588c:1.0;MAM02040c:2.0;MAM02554c:2.0;MAM02555c:-2.0;MAM02609c:1.0;MAM02630c:-2.0 MAM01365c:-2.0;MAM01588c:2.0;MAM02039c:-1.0;MAM02040c:4.0;MAM02554c:3.0;MAM02555c:-3.0;MAM02609c:2.0;MAM02630c:-4.0 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 0e2200bcf..ed2210d2b 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -203251,29 +203251,6 @@ - references: PMID:11579996;PMID:11946484;PMID:12429023;PMID:12846830;PMID:1315502;PMID:2822037;PMID:2848456;PMID:3001038;PMID:4403504;PMID:7532398;PMID:7860751;PMID:8001561 - rxnFrom: Recon3D - confidence_score: 0.0 - - !!omap - - id: MAR02023 - - name: L-Arginine, NADPH:Oxygen Oxidoreductase (Nitric-Oxide-Forming) - - metabolites: !!omap - - MAM01365c: -2.0 - - MAM01588c: 2.0 - - MAM02039c: -1.0 - - MAM02040c: 4.0 - - MAM02554c: 3.0 - - MAM02555c: -3.0 - - MAM02609c: 2.0 - - MAM02630c: -4.0 - - lower_bound: 0.0 - - upper_bound: 1000.0 - - gene_reaction_rule: ENSG00000007171 or ENSG00000089250 or ENSG00000164867 - - subsystem: - - Arginine and proline metabolism - - annotation: !!omap - - ec-code: - - 1.14.13.39 - - references: PMID:11125020;PMID:7515853 - - rxnFrom: Recon3D - - confidence_score: 0.0 - !!omap - id: MAR02026 - name: Farnesyl-Diphosphate:Farnesyl-Diphosphate Farnesyltransferase diff --git a/model/reactions.tsv b/model/reactions.tsv index 9ae3bf62e..4e540c375 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -8264,7 +8264,6 @@ MAR01975 EX_HC02161_e EX_HC02161[e] 0 EX_HC02161[e] MAR01984 EX_prpp_e EX_prpp[e] 0 EX_prpp[e] MAR01986 EX_udpg_e EX_udpg[e] 0 EX_udpg[e] MAR02021 r0093 r0093 MNXR152256 0 r0093 -MAR02023 r0145 r0145 MNXR163339 0 r0145 MAR02026 r0170 r0170 MNXR197747 0 RHEA:22673 RHEA:22672 r0170 MAR02028 R01278 ACOAR7m r0309 MNXR152845 rxn00945 0 RHEA:36144 RHEA:36143 r0309 MAR02119 r0403 r0403 MNXR163342 0 r0403 From 4721b59bcdc743aeeaa4f20eb337206ad6d817c4 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sun, 1 Nov 2026 15:46:53 +0100 Subject: [PATCH 41/44] doc: registry row for the NNK study of human lung microsomes The study has no DOI in PubMed or Crossref, so the row is keyed by its PMID. #1153 --- literature/registry.md | 1 + literature/registry.tsv | 1 + 2 files changed, 2 insertions(+) diff --git a/literature/registry.md b/literature/registry.md index aa9d0a74e..d68041d2f 100644 --- a/literature/registry.md +++ b/literature/registry.md @@ -207,6 +207,7 @@ TSV, not this file. See `README.md` for what goes in and how rows are checked. | Singh C et al. (2017). Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m116.760744](https://doi.org/10.1074/jbc.m116.760744), [PMID:27909055](https://pubmed.ncbi.nlm.nih.gov/27909055/) | Saccharomyces cerevisiae;Homo sapiens | FGGY | `MAR08726` | Ribulose changed most in a yeast YDR109C deletion, and FGGY silencing in HEK293 cells raised ribulose (seen only with ribitol added); recombinant yeast and human FGGY preferred D-ribulose over other sugars. The authors speculate a metabolite-repair role. | Abstract | enzyme assay, knockdown phenotype, metabolite measurement | abstract | Human-GEM#1171 | | Smith AG (2026). Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences. *Biomolecules*. [doi:10.3390/biom16081188](https://doi.org/10.3390/biom16081188), [PMID:42650854](https://pubmed.ncbi.nlm.nih.gov/42650854/) | multiple | CYP1A2 | `MAR04768`, `MAR04769`, `MAR04770`, `MAR04773` | Review of the oxidation of porphyrinogens to porphyrins. The review says the uroporphyrinogens are easily oxidised to the respective uroporphyrins in air, with iron and with reactive oxygen species, and that oxidation also gives non-porphyrin products such as chlorins. In mouse, Cyp1a2 knockout prevents experimental uroporphyria under the conditions reported, although uroporphyria is ultimately possible in Cyp1a2 knockout mice and Cyp1a1 knockout mice are also protected; the review says an appreciable proportion of the microsomal oxidation seems due to other CYP enzymes or processes. Reconstituted mouse CYP1A2 oxidises uroporphyrinogen, the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; it gives no stoichiometry with O2 or H2O2 and no CYP1A2 data for coproporphyrinogens, and the CYP1A2 data are from mouse and rat | Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice | review, knockout phenotype | full text | Human-GEM#1153 | | Smith G et al. (2003). Cutaneous expression of cytochrome P450 CYP2S1: individuality in regulation by therapeutic agents for psoriasis and other skin diseases. *The Lancet*. [doi:10.1016/s0140-6736(03)13081-4](https://doi.org/10.1016/s0140-6736(03)13081-4) | Homo sapiens | CYP2S1 | `MAR06700`, `MAR06701` | RT-PCR in skin of 27 healthy volunteers and 29 psoriasis patients: CYP2S1 is expressed in skin with large individual variation and is induced by UV, PUVA, coal tar and all-trans retinoic acid. The abstract reports regulation of expression, not metabolism of retinoic acid by the enzyme; the claim that CYP2S1 metabolises retinoate is not stated in the abstract and the full text was not read. | Abstract | expression, clinical | abstract | Human-GEM#1169 | +| Smith TJ et al. (1995). Activation of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in human lung microsomes by cytochromes P450, lipoxygenase, and hydroperoxides. *Cancer Research*. [PMID:7585636](https://pubmed.ncbi.nlm.nih.gov/7585636/) | Homo sapiens | | `MAR07070`, `MAR07076` | Human lung microsomes oxidise NNK, the substrate used, to keto aldehyde, keto alcohol and keto acid also without NADPH; the NADPH-independent rate is lowered by a lipoxygenase inhibitor and raised by arachidonic acid (for keto aldehyde and keto alcohol), which inhibits keto acid formation; the hydroxy acid is reported only with an NADPH-generating system. Limits: NNK is the substrate, so the conversion of the keto alcohol to the keto acid and of the diol to the hydroxy acid was not tested; the paper names no enzyme for the NADPH-independent steps | Abstract; Results; Table 1 and Table 2 | enzyme assay | full text | Human-GEM#1153 | | Sontag T, Parker R (2002). Cytochrome P450 omega-Hydroxylase Pathway of Tocopherol Catabolism. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m201466200](https://doi.org/10.1074/jbc.m201466200) | Homo sapiens;Rattus norvegicus | CYP4F2 | | Tocopherols are catabolised by P450 omega-hydroxylation of the phytyl chain followed by stepwise chain shortening to the 3'-carboxychromanol; intermediates of gamma-tocopherol were identified by GC-MS in hepatocyte cultures, and among recombinant human P450s only CYP4F2 had omega-hydroxylase activity, with higher activity for gamma- than alpha-tocopherol. Rat and human liver microsomes and cultured hepatocytes. | Abstract | enzyme assay, metabolite measurement | abstract | Human-GEM#1118, Human-GEM#1163 | | Suetake I et al. (2004). DNMT3L Stimulates the DNA Methylation Activity of Dnmt3a and Dnmt3b through a Direct Interaction. *Journal of Biological Chemistry*. [doi:10.1074/jbc.m400181200](https://doi.org/10.1074/jbc.m400181200), [PMID:15105426](https://pubmed.ncbi.nlm.nih.gov/15105426/) | Mus musculus | Dnmt3l, Dnmt3a, Dnmt3b | `MAR04072`, `MAR08640`, `MAR08641` | In vitro, human DNMT3L raised the DNA methylation activity of mouse Dnmt3a and Dnmt3b 1.5- to 3-fold, increasing with the DNMT3L amount, without affecting Dnmt1, and the effect held for all DNA substrates tested, including imprinted loci, a CpG island and synthetic polynucleotides. DNMT3L bound Dnmt3a and Dnmt3b but not DNA, and the C-terminal half carried the stimulatory effect, so the authors attribute it to a direct action on catalytic activity rather than DNA targeting. | Abstract | enzyme assay | abstract | Human-GEM#1155, animal-GEM | | Summitt CB et al. (2015). Proline dehydrogenase 2 (PRODH2) is a hydroxyproline dehydrogenase (HYPDH) and molecular target for treating primary hyperoxaluria. *Biochemical Journal*. [doi:10.1042/bj20141159](https://doi.org/10.1042/bj20141159) | Homo sapiens | PRODH2 | `MAR03838` | Purified recombinant human PRODH2 (catalytic core residues 157-515, one FAD) prefers hydroxyproline over proline, with a 12-fold higher kcat/Km, and the authors propose it uses CoQ10 as the electron acceptor in vivo and rename it HYPDH. The paper does not discuss hyperprolinaemia. | Abstract; Results (p. 4) | enzyme assay | full text | Human-GEM#1169 | diff --git a/literature/registry.tsv b/literature/registry.tsv index dc35701ed..5176582a4 100644 --- a/literature/registry.tsv +++ b/literature/registry.tsv @@ -240,3 +240,4 @@ doi pmid authors year title journal organism genes model_ids finding locator evi 10.1016/j.abb.2004.07.002 15369820 Martras S et al. 2004 Kinetics of human alcohol dehydrogenase with ring-oxidized retinoids: effect of Tween 80 Archives of Biochemistry and Biophysics Homo sapiens ADH1B;ADH4 MAR20067;MAR20068 Recombinant human ADH1B1, ADH1B2 and ADH4 acted on 4-hydroxyretinol with NAD+ (retinol oxidation assay) and on 4-oxoretinal with NADH (retinal reduction assay) at the highest rates of any retinoid tested (ADH4 kcat 2050 per min with 4-hydroxyretinol, a 3- to 40-fold increase over retinol and retinal). The authors state that the conversion of 4-hydroxyretinol and 4-oxoretinol to the corresponding retinoic acids has not been documented, and that oxidation of the ring of retinoic acid by P450s is well demonstrated. The paper does not show the oxidation of the ring 4-hydroxyl of 4-hydroxyretinol to 4-oxoretinol. Limits: in vitro with Tween 80, which inhibits competitively and raises Km about 10-fold Abstract; Results (Table 1); Discussion enzyme assay full text Human-GEM#1153 10.1021/tx980005y 9625726 Hecht SS 1998 Biochemistry, Biology, and Carcinogenicity of Tobacco-Specific N-Nitrosamines Chemical Research in Toxicology multiple MAR07070;MAR07076 Review of the metabolism of the tobacco-specific nitrosamines. It states that keto acid is formed in vivo from keto alcohol (HPB) in rats and in some in vitro systems (cultured rat oral tissue and esophagus), that keto acid is also a likely oxidation product of keto aldehyde although this does not seem to have been investigated, and that hydroxy acid arises from NNAL by further oxidation of the lactol and the diol and not by reduction of keto acid. It names no enzyme or cofactor for these oxidations. Limits: a review that cites the underlying studies; the rat data are cited from other work Sections 2.1.1.4 (alpha-methyl hydroxylation) and 2.1.3.3 (alpha-hydroxylation) review full text Human-GEM#1153 10.3390/biom16081188 42650854 Smith AG 2026 Oxidation of Uroporphyrinogens During Heme Synthesis: Role of Iron, Susceptibility and Consequences Biomolecules multiple CYP1A2 MAR04768;MAR04769;MAR04770;MAR04773 Review of the oxidation of porphyrinogens to porphyrins. The review says the uroporphyrinogens are easily oxidised to the respective uroporphyrins in air, with iron and with reactive oxygen species, and that oxidation also gives non-porphyrin products such as chlorins. In mouse, Cyp1a2 knockout prevents experimental uroporphyria under the conditions reported, although uroporphyria is ultimately possible in Cyp1a2 knockout mice and Cyp1a1 knockout mice are also protected; the review says an appreciable proportion of the microsomal oxidation seems due to other CYP enzymes or processes. Reconstituted mouse CYP1A2 oxidises uroporphyrinogen, the human enzyme is much less active, and most of the porphyrinogen oxidation in human liver microsomes is not accounted for by CYP1A2 content. Limits: a review; it gives no stoichiometry with O2 or H2O2 and no CYP1A2 data for coproporphyrinogens, and the CYP1A2 data are from mouse and rat Section 3.2 (Oxidation by Cytochrome P4501A2) and the paragraphs on Cyp1a2 knockout mice review;knockout phenotype full text Human-GEM#1153 +pmid:7585636 7585636 Smith TJ et al. 1995 Activation of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in human lung microsomes by cytochromes P450, lipoxygenase, and hydroperoxides Cancer Research Homo sapiens MAR07070;MAR07076 Human lung microsomes oxidise NNK, the substrate used, to keto aldehyde, keto alcohol and keto acid also without NADPH; the NADPH-independent rate is lowered by a lipoxygenase inhibitor and raised by arachidonic acid (for keto aldehyde and keto alcohol), which inhibits keto acid formation; the hydroxy acid is reported only with an NADPH-generating system. Limits: NNK is the substrate, so the conversion of the keto alcohol to the keto acid and of the diol to the hydroxy acid was not tested; the paper names no enzyme for the NADPH-independent steps Abstract; Results; Table 1 and Table 2 enzyme assay full text Human-GEM#1153 From a6378cd523dbfb4aa0e51e3e356143eac0cd7896 Mon Sep 17 00:00:00 2001 From: edkerk <7326655+edkerk@users.noreply.github.com> Date: Sun, 1 Nov 2026 14:59:15 +0000 Subject: [PATCH 42/44] chore: update model QC results [skip ci] --- data/testResults/balance_results.csv | 4 ++-- data/testResults/macaw_results.tsv | 4 +--- data/testResults/memote_score.md | 4 ++-- data/testResults/model_qc_comment.md | 7 +++---- data/testResults/model_qc_summary.md | 8 ++++---- data/testResults/qc_duplicate_reactions.csv | 2 -- data/testResults/qc_structure_consistency.csv | 3 --- data/thermodynamics/reactionDeltaG.tsv | 10 +++++----- 8 files changed, 17 insertions(+), 25 deletions(-) diff --git a/data/testResults/balance_results.csv b/data/testResults/balance_results.csv index 5b50d8f30..37bc2a6c2 100644 --- a/data/testResults/balance_results.csv +++ b/data/testResults/balance_results.csv @@ -3,6 +3,8 @@ MAR01065,"3-hydroxyacyl-CoA dehydrogenase (11,12-EET)",,-2 MAR01067,"3-hydroxyacyl-CoA dehydrogenase (7,8-epoxy-(4Z,10Z)-hexadecadienoic acid)",,-2 MAR01068,"3-hydroxyacyl-CoA dehydrogenase (14,15-EET)",,-2 MAR01079,fatty acid amide hydrolase (arachidonate),,-4 +MAR01185,(2E)-dodecenoyl-CoA formation (4(R)-hydroxy-dodec-(6Z)-enoate),,2 +MAR01227,(2E)-dodecenoyl-CoA formation (4(S)-hydroxy-dodec-(6Z)-enoate),,2 MAR01301,acetyl-CoA C-acyltransferase (16e-18-oxo-18-CoA-dinor-LTE4),,5 MAR01302,choloyl-CoA hydrolase (omega-COOH-tetranor-LTE3-CoA),,-3 MAR01303,acyl-CoA oxidase (omega-COOH-tetranor-LTE3-CoA),,-3 @@ -28,7 +30,6 @@ MAR01419,4-hydroperoxy-H4-neuroprostane to 4-hydroxy-E4-neuroprostane conversion MAR01427,13-hydroperoxy-H4-neuroprostane to 13-hydroxy-D4-neuroprostane conversion,,-2 MAR01430,17-hydroperoxy-H4-neuroprostane to 17-hydroxy-E4-neuroprostane conversion,,-2 MAR01431,17-hydroperoxy-H4-neuroprostane to 17-hydroxy-D4-neuroprostane conversion,,-2 -MAR02091,"17beta-estradiol-3,4-semiquinone to 17beta-estradiol-3,4-quinone conversion",,-1 MAR02443,13(S)-HPODE to 13-oxy-radical-octadecadienoate conversion,,-2 MAR02449,"12,13-epoxy-9-alkoxy-(10E)-octadecenoate hydrolysis",,-1 MAR02451,"1-hydroperoxy-8-carboxyoctyl-3,4-epoxynon-(2E)-enyl-ether to 4-oxo-2-nonenal conversion",,2 @@ -57,7 +58,6 @@ MAR04549,6-hydroxymelatonin-sulfate to 6-hydroxymelatonin conversion,,-2 MAR04552,hydroxide to melatonin radical conversion,,1 MAR04553,cyclic-3-hydroxymelatonin hydrolysis,,-1 MAR04763,heme oxygenase (biliverdin-producing) (hemoglobin),,1 -MAR04769,uroporphyrin I to uroporphyrinogen III conversion,,-6 MAR06393,hydroxide to dehydroascorbic acid conversion,,1 MAR06456,gamma-tocopheroxyl-radical to gamma-tocopherol conversion,,-1 MAR06457,8alpha-hydroxy-gamma-tocopherone to gamma-tocopheroxyl-radical conversion,,-1 diff --git a/data/testResults/macaw_results.tsv b/data/testResults/macaw_results.tsv index ec1a63a08..81a9431b0 100644 --- a/data/testResults/macaw_results.tsv +++ b/data/testResults/macaw_results.tsv @@ -393,7 +393,6 @@ MAR08546 MAM00013c + MAM02039c + MAM02555c <=> MAM02554c + MAM02785c MAM00013c o MAR03009 MAM02040x + MAM02774x --> MAM01597x + MAM02039x + MAM02772x MAM02772x ok ok ok N/A MAR03476 MAM01836x + MAM02040x --> MAM01597x + MAM01833x + MAM02039x MAM01833x ok ok ok N/A MAR08419 MAM00563c + MAM02348c <=> MAM00577c + MAM01597c MAM00563c ok ok ok N/A -MAR03321 MAM00980x + MAM01802x --> MAM01803x + MAM03543x ok MAR02818 ok ok N/A MAR07165 MAM00196c + MAM01628c --> MAM00200c + MAM02040c MAM00200c ok ok ok N/A MAR07166 MAM00200c + MAM01806c --> MAM02759c + MAM02898c MAM00200c;MAM02898c ok ok ok N/A MAR07167 MAM02040c + MAM02898c --> MAM00194c + MAM10009c MAM00194c;MAM02898c;MAM10009c ok ok ok N/A @@ -496,7 +495,7 @@ MAR00708 MAM02017c + MAM02039c + MAM02555c --> MAM00532c + MAM02554c MAM00532c;M MAR07604 MAM00512c + MAM01428c <=> MAM01590c + MAM02039c + MAM02629c MAM00512c ok ok ok N/A MAR07605 MAM02040c + MAM02629c --> MAM00627c + MAM01797c + MAM02039c MAM00627c ok ok ok N/A MAR07606 MAM00223c + MAM02040c --> MAM00224c + MAM01798c + MAM02039c MAM00224c ok ok ok N/A -MAR07607 MAM00223c + MAM02039c + MAM02040c --> MAM00222c + MAM01797c MAM00222c ok ok ok N/A +MAR07607 MAM00223c + MAM02040c --> MAM00222c + MAM01797c + MAM02039c MAM00222c ok ok ok N/A MAR08648 MAM01767r + MAM02040r --> MAM01766r + MAM02039r + MAM02470r MAM01766r;MAM02470r ok ok ok N/A MAR01716 MAM01434x + MAM02040x --> MAM01435x + MAM01597x + MAM02039x MAM01435x ok ok ok N/A MAR01778 MAM01179r + MAM02039r + MAM02553r <=> MAM01447r + MAM02552r MAM01179r ok ok ok N/A @@ -1249,7 +1248,6 @@ MAR02763 MAM02040l + MAM02762l <=> MAM02039l + MAM02763l + MAM02946l MAM02762l;M MAR02765 MAM01306m + MAM02319m --> MAM00990m + MAM01974m + MAM02040m MAM00990m;MAM02319m ok ok ok N/A MAR02786 MAM01371m + MAM01597m + MAM02387m --> MAM01334m + MAM02391m + MAM02759m MAM02387m ok ok ok N/A MAR02802 MAM01371x + MAM01597x + MAM02387x --> MAM01334x + MAM02391x + MAM02759x MAM02387x ok ok ok N/A -MAR02818 MAM00980x + MAM01802x --> MAM01803x + MAM03543x ok MAR03321 ok ok N/A MAR02820 MAM00081c + MAM02552c <=> MAM00855c + MAM02039c + MAM02553c MAM00081c;MAM00855c ok ok ok N/A MAR02826 MAM00696c + MAM02552c <=> MAM00854c + MAM02039c + MAM02553c MAM00696c;MAM00854c ok ok ok N/A MAR02828 MAM00082c + MAM02552c <=> MAM00883c + MAM02039c + MAM02553c MAM00082c;MAM00883c ok ok ok N/A diff --git a/data/testResults/memote_score.md b/data/testResults/memote_score.md index d11ce3fa9..2a1ebb6b9 100644 --- a/data/testResults/memote_score.md +++ b/data/testResults/memote_score.md @@ -4,7 +4,7 @@ Mode: core subset. -Model version: 49719187a1a2. +Model version: 5a4453204772. Skipped (slow) tests: test_stoichiometric_consistency, test_unconserved_metabolites, test_inconsistent_min_stoichiometry, test_detect_energy_generating_cycles, test_find_stoichiometrically_balanced_cycles, test_blocked_reactions, test_find_reactions_unbounded_flux_default_condition, test_find_metabolites_not_produced_with_open_bounds, test_find_metabolites_not_consumed_with_open_bounds, test_number_independent_conservation_relations, test_matrix_rank, test_degrees_of_freedom. **Total score: 63.9%** @@ -24,7 +24,7 @@ Skipped (slow) tests: test_stoichiometric_consistency, test_unconserved_metaboli | Section | Test | Score | | --- | --- | ---: | | Consistency | Mass Balance | 99.4% | -| Consistency | Charge Balance | 98.7% | +| Consistency | Charge Balance | 98.8% | | Consistency | Metabolite Connectivity | 100.0% | | Annotation - Metabolites | Presence of Metabolite Annotation | 100.0% | | Annotation - Metabolites | Metabolite Annotations Per Database | 47.1% | diff --git a/data/testResults/model_qc_comment.md b/data/testResults/model_qc_comment.md index a3760a95e..ddb580456 100644 --- a/data/testResults/model_qc_comment.md +++ b/data/testResults/model_qc_comment.md @@ -1,22 +1,21 @@ ## Model quality report -:x: **3** regression(s) vs `develop`. Review the row(s) below. Gates: duplicate keys **0** :white_check_mark:, growth **1.9** :white_check_mark:, direction alarms **0** :white_check_mark:. +:x: **1** regression(s) vs `develop`. Review the row(s) below. Gates: duplicate keys **0** :white_check_mark:, growth **1.9** :white_check_mark:, direction alarms **0** :white_check_mark:. | Section | Status | | --- | --- | -| Model & network checks (24) | :x: **3** regression(s) | +| Model & network checks (24) | :x: **1** regression(s) | | Model file & metabolic tasks (8) | :white_check_mark: all pass | | MEMOTE | :sparkles: **63.9%** (core subset) | | Full report | [model_qc_summary.md](model_qc_summary.md) | **Regression(s):** -- Exact-duplicate reaction groups: [**1**](qc_duplicate_reactions.csv) -- Reactions flagged as MACAW duplicates: [**340**](macaw_results.tsv) - Reactions flagged by MACAW dead-end test: [**1382**](macaw_results.tsv) **Improved:** - Mass-imbalanced reactions: **0** - Charge-imbalanced reactions: [**87**](balance_results.csv) +- Structure vs formula/charge inconsistencies: [**48**](qc_structure_consistency.csv) :white_check_mark: unchanged · :sparkles: improved vs `develop` · :warning: pre-existing, non-blocking · :x: regression diff --git a/data/testResults/model_qc_summary.md b/data/testResults/model_qc_summary.md index 33ff5b886..67803f324 100644 --- a/data/testResults/model_qc_summary.md +++ b/data/testResults/model_qc_summary.md @@ -30,15 +30,15 @@ _Reaction directions: the alarm and the warning catch only directions that therm | [Metabolites missing charge](README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: | | [Mass-imbalanced reactions](README.md#mass-imbalanced-reactions) | 0 | -65 | :sparkles: | | [Charge-imbalanced reactions](README.md#charge-imbalanced-reactions) | [87](balance_results.csv) | -58 | :sparkles: | -| [Structure vs formula/charge inconsistencies](README.md#structure-vs-formulacharge-inconsistencies) | [51](qc_structure_consistency.csv) | 0 | :warning: | +| [Structure vs formula/charge inconsistencies](README.md#structure-vs-formulacharge-inconsistencies) | [48](qc_structure_consistency.csv) | -3 | :sparkles: | #### Network structure | Check | Result | Δ vs `develop` | | | --- | ---: | ---: | :---: | | [Reactions with no metabolites](README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: | -| [Exact-duplicate reaction groups](README.md#exact-duplicate-reaction-groups) | [1](qc_duplicate_reactions.csv) | +1 | :x: | -| [Reactions flagged as MACAW duplicates](README.md#reactions-flagged-as-macaw-duplicates) | [340](macaw_results.tsv) | +2 | :x: | +| [Exact-duplicate reaction groups](README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: | +| [Reactions flagged as MACAW duplicates](README.md#reactions-flagged-as-macaw-duplicates) | [338](macaw_results.tsv) | 0 | :warning: | | [Twin reactions with a missing or conflicting EC number](README.md#twin-reactions-with-a-missing-or-conflicting-ec-number) | 0 | 0 | :white_check_mark: | | [Reactions flagged by MACAW dead-end test](README.md#reactions-flagged-by-macaw-dead-end-test) | [1382](macaw_results.tsv) | +2 | :x: | | [Reactions split across compartments](README.md#reactions-split-across-compartments) | [26](qc_split_compartments.csv) | 0 | :warning: | @@ -86,7 +86,7 @@ _Reaction directions: the alarm and the warning catch only directions that therm | Section | Test | Score | | --- | --- | ---: | | Consistency | Mass Balance | 99.4% | -| Consistency | Charge Balance | 98.7% | +| Consistency | Charge Balance | 98.8% | | Consistency | Metabolite Connectivity | 100.0% | | Annotation - Metabolites | Presence of Metabolite Annotation | 100.0% | | Annotation - Metabolites | Metabolite Annotations Per Database | 47.1% | diff --git a/data/testResults/qc_duplicate_reactions.csv b/data/testResults/qc_duplicate_reactions.csv index 99d7215fb..c10c4ef6a 100644 --- a/data/testResults/qc_duplicate_reactions.csv +++ b/data/testResults/qc_duplicate_reactions.csv @@ -1,3 +1 @@ group,reaction,equation -1,MAR02818,MAM00980x + MAM01802x --> MAM01803x + MAM03543x -1,MAR03321,MAM00980x + MAM01802x --> MAM01803x + MAM03543x diff --git a/data/testResults/qc_structure_consistency.csv b/data/testResults/qc_structure_consistency.csv index 4408f7b2a..2947a6ae1 100644 --- a/data/testResults/qc_structure_consistency.csv +++ b/data/testResults/qc_structure_consistency.csv @@ -1,13 +1,10 @@ mets,name,issue,model_formula,model_charge,smiles_formula,smiles_charge,metSmiles MAM00031c,"(1R)-hydroxy-(2R)-glutathionyl-1,2-dihydronaphthalene",protonation,C20H23N3O7S,-2.0,C20H25N3O7S,0,N[C@@H](CCC(=O)N[C@@H](CS[C@@H]1C=Cc2ccccc2[C@H]1O)C(=O)NCC(=O)O)C(=O)O MAM00033c,"(1S)-hydroxy-(2S)-glutathionyl-1,2-dihydronaphthalene",protonation,C20H23N3O7S,-2.0,C20H25N3O7S,0,N[C@@H](CCC(=O)N[C@@H](CS[C@H]1C=Cc2ccccc2[C@@H]1O)C(=O)NCC(=O)O)C(=O)O -MAM00229c,"1,2,3,4-tetrahydro-alpha,7-dihydroxy-beta-(hydroxymethyl)-9-methoxy-3,4-dioxocyclopenta[c][1]benzopyran-6-propanal",protonation,C17H15O8,-1.0,C17H16O8,0,COc1cc(O)c(C(CO)C(O)C=O)c2oc(=O)c3c(c12)CCC3=O MAM00397x,16(S)-hydroxy-18-oxo-18-CoA-LTE4,protonation,C42H62N8O23P3S2,-5.0,C42H63N8O23P3S2-4,-4,CC(C)(COP(=O)([O-])OP(=O)([O-])OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]1OP(=O)([O-])[O-])C(O)C(=O)NCCC(=O)NCCSC(=O)C[C@@H](O)CCC/C=C\C=C\C=C\[C@@H](SC[C@@H](N)C(=O)O)[C@@H](O)CCCC(=O)O MAM00557c,1-pyrroline,protonation,C4H8N,1.0,C4H7N,0,C1=NCCC1 MAM00557m,1-pyrroline,protonation,C4H8N,1.0,C4H7N,0,C1=NCCC1 MAM00912c,3-phosphoadenylylselenate,protonation,C10H11N5O13P2Se,-4.0,C10H15N5O13P2Se,0,Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O[Se](=O)(=O)O)[C@@H](OP(=O)(O)O)[C@H]1O -MAM01294c,aflatoxin B1 dialdehyde,protonation,C17H13O8,-1.0,C17H14O8,0,COc1cc(O)c([C@@H](C=O)[C@@H](O)C=O)c2oc(=O)c3c(c12)CCC3=O -MAM01318c,"alpha-(1,2-dihydroxyethyl)-1,2,3,4-tetrahydro-7-hydroxy-9-methoxy-3,4-dioxocyclopenta[c][1]benzopyran-6-acetaldehyde",protonation,C17H15O8,-1.0,C17H16O8,0,COc1cc(O)c(C(C=O)C(O)CO)c2oc(=O)c3c(c12)CCC3=O MAM01367c,arsenite,protonation,AsH2O3,-1.0,AsO3-3,-3,[O-][As]([O-])[O-] MAM01402c,biotinyl-5-AMP,protonation,C20H27N7O9PS,-1.0,C20H28N7O9PS,0,Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)OC(=O)CCCC[C@@H]2SC[C@@H]3NC(=O)N[C@H]23)[C@@H](O)[C@H]1O MAM01591c,CMP-2-aminoethylphosphonate,protonation,C11H19N4O10P2,-1.0,C11H20N4O10P2,0,NCCP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2ccc(N)nc2=O)[C@H](O)[C@@H]1O diff --git a/data/thermodynamics/reactionDeltaG.tsv b/data/thermodynamics/reactionDeltaG.tsv index b2c66f664..e4c54c0d8 100644 --- a/data/thermodynamics/reactionDeltaG.tsv +++ b/data/thermodynamics/reactionDeltaG.tsv @@ -799,7 +799,6 @@ MAR02019 r single 2.4 1.6 0c3a5dcc2a MAR02020 c single 141.9 70714.9 bca22d7ca8 MAR02021 e single -56.7 3.8 b72444b6c8 MAR02022 c single 2.3 1.6 64c93a4c3a -MAR02023 c single -1221.9 15.1 77a764f643 MAR02024 r single 2.3 1.6 1ec2faca2d MAR02025 c single -141.9 70714.9 2082ba7458 MAR02026 r single -157.1 7.8 8839abbba2 @@ -2314,6 +2313,7 @@ MAR04764 c single 22.0 9.9 a9cbcaa95c MAR04766 r single 8.1 5.1 079f7c2185 MAR04767 r single -0.0 0.0 677f7242b1 MAR04768 c single -0.0 100000.0 d2a9d07549 +MAR04769 c single -0.0 100000.0 dc941809c2 MAR04770 c single -0.0 100000.0 18ff4ea1a4 MAR04771 c single -314.0 400035.1 3e98478f19 MAR04772 c single -97.7 12.4 2c75539da1 @@ -2709,8 +2709,8 @@ MAR07020 c single -736.0 62807.6 392de3f1df MAR07021 c single -736.0 62807.6 2a449713ef MAR07022 c single 370.5 62806.5 c0fef51d23 MAR07023 c single 374.7 62806.4 59aad51ced -MAR07026 c single -17.8 1.0 cf21a78018 -MAR07028 c single -17.6 1.0 48251991d4 +MAR07026 c single -17.8 1.0 626de29f71 +MAR07028 c single -17.6 1.0 deaec6c6bb MAR07029 c single -42.7 100000.0 7738bf5b48 MAR07030 c single -400.2 6.4 699187e157 MAR07031 c single 0.0 100000.0 9884697289 @@ -2747,9 +2747,9 @@ MAR07066 c single 41.8 100000.0 2836ee39d4 MAR07067 c single 64.8 100000.0 201660957b MAR07068 c single -17.1 100000.0 5ce1f2d65c MAR07069 c single -17.1 100000.0 a7ef577fe3 -MAR07070 c single -458.3 3.1 a26e21451d +MAR07070 c single -458.3 3.1 c2fc3f85d2 MAR07071 c single -17.1 100000.0 1653bc8f0b -MAR07072 c single -477.6 3.1 5d3a8b028c +MAR07072 c single -477.6 3.1 265a683020 MAR07073 c single -17.1 100000.0 925333e60c MAR07074 c single -494.3 4.3 d831f426e6 MAR07075 c single -17.1 100000.0 8bf2795140 From 1160aed589781eae7667ad0242a9f0167e9b829e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun, 1 Nov 2026 15:38:53 +0000 Subject: [PATCH 43/44] chore: add gene essentiality test result [skip ci] --- data/testResults/gene-essential-diff.csv | 1873 +++++++++++++++++++- data/testResults/gene-essential.csv | 186 +- data/testResults/gene-essential_summary.md | 21 +- 3 files changed, 1955 insertions(+), 125 deletions(-) diff --git a/data/testResults/gene-essential-diff.csv b/data/testResults/gene-essential-diff.csv index d4851899d..742e26397 100644 --- a/data/testResults/gene-essential-diff.csv +++ b/data/testResults/gene-essential-diff.csv @@ -1,59 +1,1890 @@ 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+ENSG00000274588,DGKK,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000276293,PIP4K2B,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000276747,PADI6,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, +ENSG00000277893,SRD5A2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000278540,ACACA,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 +ENSG00000284844,TOMT,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000288702,UGT1A3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000288705,UGT1A5,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000291237,SOD2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv index 63860dbb3..bcb6e87aa 100644 --- a/data/testResults/gene-essential.csv +++ b/data/testResults/gene-essential.csv @@ -66,7 +66,7 @@ ENSG00000011275,RNF216,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000011405,PIK3C2A,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000012232,EXTL3,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000012660,ELOVL5,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000012779,ALOX5,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,0.999997,TN,,1.000000 +ENSG00000012779,ALOX5,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,0.999990,TN,,1.000000 ENSG00000012963,UBR7,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000013288,MAN2B2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000013306,SLC25A39,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -96,12 +96,12 @@ ENSG00000023041,ZDHHC6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000023228,NDUFS1,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000023330,ALAS1,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000023572,GLRX2,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000023697,DERA,TN,,0.666813,TN,,0.666813,TN,,0.666813,TN,,0.666813,TN,,1.000000 +ENSG00000023697,DERA,TN,,0.666810,TN,,0.666810,TN,,0.666810,TN,,0.666810,TN,,1.000000 ENSG00000023839,ABCC2,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000023909,GCLM,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000024048,UBR2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000025423,HSD17B6,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000025708,TYMP,TN,,0.666754,TN,,0.666754,TN,,0.666754,TN,,0.666754,TN,.,. +ENSG00000025708,TYMP,TN,,0.666752,TN,,0.666752,TN,,0.666752,TN,,0.666752,TN,.,. ENSG00000025800,KPNA6,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000026652,AGPAT4,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000027847,B4GALT7,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 @@ -117,7 +117,7 @@ ENSG00000033867,SLC4A7,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1 ENSG00000034677,RNF19A,TN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000035687,ADSS2,.,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,FP,BS|GR,0.000000 ENSG00000036473,OTC,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000036530,CYP46A1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. +ENSG00000036530,CYP46A1,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000036565,SLC18A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000036672,USP2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000037757,MRI1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -139,7 +139,7 @@ ENSG00000048392,RRM2B,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,B ENSG00000049239,H6PD,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000049759,NEDD4L,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000049860,HEXB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000050438,SLC4A8,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 +ENSG00000050438,SLC4A8,TN,,1.000000,TN,,0.968499,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000051341,POLQ,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000051382,PIK3CB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000052802,MSMO1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -151,7 +151,7 @@ ENSG00000054983,GALC,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000055483,USP36,FN,.,.,FN,.,.,FN,.,.,TN,.,.,FN,.,. ENSG00000055609,KMT2C,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000056998,GYG2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000057252,SOAT1,TN,,0.978662,TN,,0.978663,TN,,0.978686,TN,,0.978666,TN,,0.978655 +ENSG00000057252,SOAT1,TN,,0.999918,TN,,1.000000,TN,,0.999918,TN,,0.999918,TN,,1.000000 ENSG00000058056,USP13,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000058600,POLR3E,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 ENSG00000058668,ATP2B4,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -167,7 +167,7 @@ ENSG00000060971,ACAA1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1. ENSG00000060982,BCAT1,TN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000,FN,,1.000000 ENSG00000061918,GUCY1B1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000062282,DGAT2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000062485,CS,FP,BS|ER|IC|SU,1.000000,TP,BS|ER|IC,1.000000,FP,ER|IC,1.000000,FP,BS|ER|IC|SU,1.000000,FP,BS|ER|IC|SU,1.000000 +ENSG00000062485,CS,FP,BS|ER|IC,1.000000,TP,BS|ER|IC,1.000000,FP,ER|IC,1.000000,FP,BS|ER|IC|SU,1.000000,FP,BS|ER|IC|SU,1.000000 ENSG00000062822,POLD1,FN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000063176,SPHK2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000063601,MTMR1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -199,13 +199,13 @@ ENSG00000067057,PFKP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.0 ENSG00000067064,IDI1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000067113,PLPP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000067177,PHKA1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. -ENSG00000067225,PKM,FN,,0.666699,TN,,0.666699,FN,,0.666699,FN,,0.666699,FN,,0.500024 +ENSG00000067225,PKM,FN,,0.666698,TN,,0.666698,FN,,0.666698,FN,,0.666698,FN,,0.500024 ENSG00000067829,IDH3G,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000067840,PDZD4,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000067842,ATP2B3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000067992,PDK3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000068001,HYAL2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000068120,COASY,TP,BS|GR,-0.000000,FP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000 +ENSG00000068120,COASY,TP,BS|GR,0.000000,FP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000 ENSG00000068308,OTUD5,TN,.,.,FN,.,.,TN,.,.,TN,.,.,FN,.,. ENSG00000068366,ACSL4,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000068383,INPP5A,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -250,7 +250,7 @@ ENSG00000072682,P4HA2,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000072778,ACADVL,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,1.000000 ENSG00000073060,SCARB1,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000073417,PDE8A,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000073578,SDHA,TP,BS|ER|SU,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,TP,BS|ER|SU,1.000000 +ENSG00000073578,SDHA,TP,ER,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,TP,BS|ER|SU,1.000000 ENSG00000073734,ABCB11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000073737,DHRS9,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000073756,PTGS2,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 @@ -311,7 +311,7 @@ ENSG00000081800,SLC13A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,, ENSG00000081923,ATP8B1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000082212,ME2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000082996,RNF13,.,.,.,.,.,.,TN,.,.,TN,.,.,.,.,. -ENSG00000083123,BCKDHB,TN,,0.999952,TN,,0.999704,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999704 +ENSG00000083123,BCKDHB,TN,,0.999953,TN,,0.999669,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999669 ENSG00000083168,KAT6A,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000083223,TUT7,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000083444,PLOD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 @@ -369,7 +369,7 @@ ENSG00000089472,HEPH,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000089597,GANAB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000090013,BLVRB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000090020,SLC9A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000090054,SPTLC1,TN,,0.999777,TN,,0.999777,TN,,0.999777,TN,,0.999777,TN,,0.999777 +ENSG00000090054,SPTLC1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000090060,PAPOLA,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000090266,NDUFB2,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000090402,SI,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. @@ -380,8 +380,8 @@ ENSG00000090861,AARS1,TP,BS|GR,0.000000,FP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,B ENSG00000090971,NAT14,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000091137,SLC26A4,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000 ENSG00000091138,SLC26A3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000091140,DLD,TP,ER,0.996886,TP,ER,0.996573,TP,ER|GR,0.000000,FP,BS|ER|GR,0.000000,TP,BS|ER|IC|SU,0.996573 -ENSG00000091483,FH,TP,BS|ER|GR|SU,-0.000000,FP,BS|ER,1.000000,TP,BS|ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 +ENSG00000091140,DLD,TP,ER,0.989270,TP,ER,0.988929,TP,ER|GR,0.000000,FP,BS|ER|GR,0.000000,TP,BS|ER|IC|SU,0.988928 +ENSG00000091483,FH,TP,BS|ER,1.000000,FP,BS|ER,1.000000,TP,BS|ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 ENSG00000091664,SLC17A6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000091704,CPA1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000092009,CMA1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -400,7 +400,7 @@ ENSG00000095059,DHPS,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.0 ENSG00000095139,ARCN1,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000095303,PTGS1,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000095319,NUP188,TP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 -ENSG00000095321,CRAT,FP->TN,BS|SU,0.978662,FP->TN,BS|SU,0.978663,FP->TN,BS|SU,0.978686,FP->TN,BS|SU,0.978666,FP->TN,BS|SU,0.978655 +ENSG00000095321,CRAT,FP->TN,BS|SU,0.999918,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,0.999918,FP->TN,BS|SU,0.999918,FP->TN,BS|SU,1.000000 ENSG00000095380,NANS,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000095464,PDE6C,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000095596,CYP26A1,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000 @@ -414,7 +414,7 @@ ENSG00000097033,SH3GLB1,TN,.,.,TN,.,.,TN,.,.,FN,.,.,TN,.,. ENSG00000099194,SCD,FN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000099377,HSD3B7,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000099381,SETD1A,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 -ENSG00000099624,ATP5F1D,TP,ER,0.996911,TP,ER,0.996907,TP,ER,0.996890,TP,ER,0.996887,TP,ER,0.993707 +ENSG00000099624,ATP5F1D,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,TP,ER,0.986210 ENSG00000099785,MARCHF2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000099795,NDUFB7,FN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000099797,TECR,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000 @@ -458,20 +458,19 @@ ENSG00000100417,PMM1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.0 ENSG00000100422,CERK,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000100442,FKBP3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FN,.,. ENSG00000100448,CTSG,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000100479,POLE2,FN,.,.,FN,.,.,FN,.,.,FN,.,.,FN,.,. ENSG00000100504,PYGL,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000100522,GNPNAT1,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000100554,ATP6V1D,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000100564,PIGH,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000100577,GSTZ1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000100596,SPTLC2,TN,,0.999777,FN,,0.999777,TN,,0.999777,TN,,0.999777,FN,,0.999777 +ENSG00000100596,SPTLC2,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000100600,LGMN,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000100605,ITPK1,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000100626,GALNT16,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000100644,HIF1A,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000100652,SLC10A1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000100678,SLC8A3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000100714,MTHFD1,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000 +ENSG00000100714,MTHFD1,TP->FN,BS,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000100814,CCNB1IP1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000100867,DHRS2,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000100889,PCK2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -516,7 +515,7 @@ ENSG00000102032,RENBP,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000102043,MTMR8,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000102078,SLC25A14,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000102100,SLC35A2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000102144,PGK1,FN,,0.666674,FN,,0.666674,FN,,0.666674,FN,,0.666674,FN,,0.500006 +ENSG00000102144,PGK1,FN,,0.666674,FN,,0.666674,FN,,0.666674,FN,,0.666674,FN,,0.500005 ENSG00000102172,SMS,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000102226,USP11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000102230,PCYT1B,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. @@ -529,7 +528,7 @@ ENSG00000102575,ACP5,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000102699,PARP4,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000102743,SLC25A15,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000102780,DGKH,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000102794,ACOD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 +ENSG00000102794,ACOD1,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000102858,MGRN1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000102893,PHKB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000102900,NUP93,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 @@ -569,7 +568,7 @@ ENSG00000104044,OCA2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.0 ENSG00000104055,TGM5,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000104219,ZDHHC2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FN,.,. ENSG00000104267,CA2,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. -ENSG00000104325,DECR1,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,0.999997,FP->TN,SU,1.000000 +ENSG00000104325,DECR1,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,0.999990,FP->TN,SU,1.000000 ENSG00000104331,BPNT2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000104343,UBE2W,.,.,.,.,.,.,TN,.,.,TN,.,.,.,.,. ENSG00000104517,UBR5,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -577,7 +576,7 @@ ENSG00000104522,GFUS,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.0 ENSG00000104524,PYCR3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000104549,SQLE,FP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 ENSG00000104635,SLC39A14,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000104687,GSR,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,0.999998,TN,,1.000000 +ENSG00000104687,GSR,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,0.999992,TN,,1.000000 ENSG00000104723,TUSC3,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000104763,ASAH1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000104774,MAN2B1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -586,7 +585,7 @@ ENSG00000104812,GYS1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.0 ENSG00000104823,ECH1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000104879,CKM,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. ENSG00000104885,DOT1L,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 -ENSG00000104888,SLC17A7,TN,.,.,FN,.,.,TN,,1.000000,TN,.,.,TN,.,. +ENSG00000104888,SLC17A7,TN,.,.,FN,.,.,TN,,0.999890,TN,.,.,TN,.,. ENSG00000104907,TRMT1,FN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000104951,IL4I1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000105143,SLC1A6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -613,7 +612,7 @@ ENSG00000105675,ATP4A,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000105679,GAPDHS,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000105701,FKBP8,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000105755,ETHE1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000105835,NAMPT,TN,,1.000000,FP,GR,-0.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 +ENSG00000105835,NAMPT,TN,,1.000000,FP,GR,0.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000105851,PIK3CG,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000105852,PON3,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000105854,PON2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -637,7 +636,7 @@ ENSG00000106605,BLVRA,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000106628,POLD2,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000106633,GCK,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000106688,SLC1A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,. -ENSG00000106733,NMRK1,TN,,0.999969,TN,.,.,TN,,0.999969,TN,,0.999969,TN,,0.999969 +ENSG00000106733,NMRK1,TN,,0.999970,TN,.,.,TN,,0.999970,TN,,0.999970,TN,,0.999970 ENSG00000106853,PTGR1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000106976,DNM1,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000106992,AK1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -650,7 +649,7 @@ ENSG00000107537,PHYH,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.0 ENSG00000107611,CUBN,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000107669,ATE1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FN,.,. ENSG00000107789,MINPP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000107798,LIPA,TN,,0.978742,TN,,1.000000,TN,,1.000000,TN,,0.978746,TN,,0.978735 +ENSG00000107798,LIPA,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000107819,SFXN3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000107854,TNKS2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000107902,LHPP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -673,7 +672,7 @@ ENSG00000108773,KAT2A,TN,.,.,FN,.,.,TN,.,.,FN,.,.,FN,.,. ENSG00000108784,NAGLU,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000108786,HSD17B1,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000108799,EZH1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000108839,ALOX12,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,0.999997,TN,,1.000000 +ENSG00000108839,ALOX12,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,0.999990,TN,,1.000000 ENSG00000108846,ABCC3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000108854,SMURF2,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. ENSG00000108932,SLC16A6,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000 @@ -723,13 +722,13 @@ ENSG00000110871,COQ5,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 ENSG00000110887,DAO,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000110911,SLC11A2,FP,BS|GR,0.000000,TN,,1.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,TN,,1.000000 ENSG00000110921,MVK,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000 -ENSG00000110955,ATP5F1B,TP,ER,0.996911,TP,ER,0.996907,TP,ER,0.996890,TP,ER,0.996887,TP,ER,0.993707 +ENSG00000110955,ATP5F1B,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,TP,ER,0.986210 ENSG00000110958,PTGES3,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000111012,CYP27B1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000111058,ACSS3,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000 ENSG00000111077,TNS2,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000111144,LTA4H,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000111181,SLC6A12,TN,.,.,FN,.,.,TN,,1.000000,TN,.,.,TN,.,. +ENSG00000111181,SLC6A12,TN,.,.,FN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000111224,PARP11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000111261,MANSC1,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000111275,ALDH2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -738,10 +737,10 @@ ENSG00000111339,ART4,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000111371,SLC38A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000111445,RFC5,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000111581,NUP107,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 -ENSG00000111640,GAPDH,.,,0.501952,.,,0.557725,FN,,0.557725,FN,,1.000000,.,,0.500000 +ENSG00000111640,GAPDH,.,,0.501911,.,,0.557690,FN,,0.557678,FN,,1.000000,.,,0.500000 ENSG00000111666,CHPT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000111667,USP5,FN,.,.,FN,.,.,FN,.,.,FN,.,.,FN,.,. -ENSG00000111669,TPI1,TN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,0.670273 +ENSG00000111669,TPI1,TN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,0.670223 ENSG00000111670,GNPTAB,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000111674,ENO2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000111684,LPCAT3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -775,7 +774,7 @@ ENSG00000112499,SLC22A2,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000112541,PDE10A,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000112695,COX7A2,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000 ENSG00000112699,GMDS,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000112759,SLC29A1,TN,,0.998235,TN,,0.998235,TN,,0.998235,TN,,0.998235,TN,,0.998322 +ENSG00000112759,SLC29A1,TN,,0.998273,TN,,0.998273,TN,,0.998273,TN,,0.998273,TN,,0.998358 ENSG00000112874,NUDT12,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000112893,MAN2A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000112941,TENT4A,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -809,7 +808,7 @@ ENSG00000114054,PCCB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.0 ENSG00000114062,UBE3A,TN,.,.,TN,.,.,TN,.,.,FN,.,.,TN,.,. ENSG00000114113,RBP2,FP,GR,0.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000114115,RBP1,TN,.,.,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 -ENSG00000114120,SLC25A36,FP,GR,0.000000,TN,,0.998326,TN,,0.998327,FP,GR,0.000000,FP,GR,0.000000 +ENSG00000114120,SLC25A36,FP,GR,0.000000,TN,,0.998362,TN,,0.998362,FP,GR,0.000000,FP,GR,0.000000 ENSG00000114124,GRK7,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000114166,KAT2B,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000114200,BCHE,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000 @@ -871,12 +870,12 @@ ENSG00000116171,SCP2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.0 ENSG00000116199,FAM20B,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000116237,ICMT,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000116337,AMPD2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000116353,MECR,FN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,0.999997,FN,,1.000000 -ENSG00000116459,ATP5PB,TP,ER,0.996911,TP,ER,0.996907,TP,ER,0.996890,TP,ER,0.996887,FP,ER,0.993707 +ENSG00000116353,MECR,FN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,0.999990,FN,,1.000000 +ENSG00000116459,ATP5PB,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,FP,ER,0.986210 ENSG00000116514,RNF19B,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000116539,ASH1L,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000116649,SRM,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000116704,SLC35D1,FP,GR,0.000000,TN,,1.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 +ENSG00000116704,SLC35D1,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,TN,,1.000000 ENSG00000116711,PLA2G4A,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000116745,RPE65,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000116748,AMPD1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -890,7 +889,7 @@ ENSG00000117009,KMO,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000117054,ACADM,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP->TN,BS,1.000000 ENSG00000117069,ST6GALNAC5,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000117115,PADI2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000117118,SDHB,TP,BS|ER|SU,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 +ENSG00000117118,SDHB,TP,ER,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 ENSG00000117143,UAP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000117215,PLA2G2D,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000117305,HMGCL,TN,,1.000000,TN,,1.000000,TN,,0.999990,TN,,0.999990,TN,,1.000000 @@ -935,10 +934,10 @@ ENSG00000119401,TRIM32,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000119421,NDUFA8,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000119514,GALNT12,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000119523,ALG2,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 -ENSG00000119537,KDSR,FN,,0.999777,TN,,0.999777,FN,,0.999777,FN,,0.999777,FN,,0.999777 +ENSG00000119537,KDSR,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000119640,ACYP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000119673,ACOT2,TN,,1.000000,FN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 -ENSG00000119689,DLST,TP,ER,1.000000,FP,ER,0.998813,TP,ER,0.998797,TP,ER,0.998795,FP,BS|ER|IC|SU,0.998812 +ENSG00000119689,DLST,TP,ER,1.000000,FP,ER,0.998838,TP,ER,0.998823,TP,ER,1.000000,FP,BS|ER|IC|SU,0.998838 ENSG00000119711,ALDH6A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP,GR,0.000000,TN,,1.000000 ENSG00000119723,COQ6,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000119772,DNMT3A,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FN,.,. @@ -953,9 +952,9 @@ ENSG00000120253,NUP43,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,TP,GR,0.00000 ENSG00000120254,MTHFD1L,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000120265,PCMT1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000120329,SLC25A2,TN,,1.000000,TN,,1.000000,FP,GR,0.000000,FP,GR,0.000000,TN,,1.000000 -ENSG00000120437,ACAT2,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP->TN,BS,0.994466,FP->TN,BS,0.994466,FP,BS|GR,0.000000 +ENSG00000120437,ACAT2,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP->TN,BS,0.994583,FP->TN,BS,0.994583,FP,BS|GR,0.000000 ENSG00000120563,LYZL1,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. -ENSG00000120697,ALG5,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 +ENSG00000120697,ALG5,TN,,0.999992,TN,,0.999992,TN,,1.000000,TN,,0.999991,TN,,0.999990 ENSG00000120820,GLT8D2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000120915,EPHX2,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000120942,UBIAD1,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. @@ -1013,7 +1012,7 @@ ENSG00000124140,SLC12A5,TN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000124151,NCOA3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000124155,PIGT,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000124164,VAPB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000124172,ATP5F1E,P,ER,0.996911,P,ER,0.996907,P,ER,0.996890,P,ER,0.996887,P,ER,0.993707 +ENSG00000124172,ATP5F1E,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 ENSG00000124181,PLCG1,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000124212,PTGIS,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000124253,PCK1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1048,7 +1047,7 @@ ENSG00000125484,GTF3C4,FN,.,.,TN,.,.,FN,.,.,TN,.,.,FN,.,. ENSG00000125505,MBOAT7,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. ENSG00000125630,POLR1B,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 ENSG00000125772,GPCPD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000125779,PANK2,TN,,0.999813,TN,,0.999813,TN,,0.999813,TN,,0.999813,TN,,0.999813 +ENSG00000125779,PANK2,TN,,0.999817,TN,,0.999817,TN,,0.999817,TN,,0.999817,TN,,0.999817 ENSG00000125780,TGM3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000125877,ITPA,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000126088,UROD,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 @@ -1061,7 +1060,7 @@ ENSG00000126522,ASL,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.00 ENSG00000126821,SGPP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000126883,NUP214,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 ENSG00000127080,IPPK,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000127125,PPCS,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 +ENSG00000127125,PPCS,FP,BS|GR,-0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 ENSG00000127184,COX7C,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000 ENSG00000127412,TRPV5,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000127415,IDUA,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1198,7 +1197,7 @@ ENSG00000133027,PEMT,FP->TN,BS,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,T ENSG00000133056,PIK3C2B,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000133063,CHIT1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000133065,SLC41A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000133116,KL,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. +ENSG00000133116,KL,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FP,GR,0.000000 ENSG00000133121,STARD13,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000133135,RNF128,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000133247,KMT5C,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1253,9 +1252,9 @@ ENSG00000135220,UGT2A3,.,,1.000000,.,.,.,TN,,1.000000,TN,,1.000000,.,.,. ENSG00000135226,UGT2B28,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000135241,PNPLA8,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000135318,NT5E,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000135390,ATP5MC2,FP,ER,0.996911,FP,ER,0.996907,TP,ER,0.996890,TP,ER,0.996887,FP,ER,0.993707 +ENSG00000135390,ATP5MC2,FP,ER,0.989294,FP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,FP,ER,0.986210 ENSG00000135423,GLS2,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,.,. -ENSG00000135437,RDH5,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 +ENSG00000135437,RDH5,TN,,1.000000,FN,,1.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 ENSG00000135454,B4GALNT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000135587,SMPD2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000135655,USP15,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1271,7 +1270,7 @@ ENSG00000135845,PIGC,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.0 ENSG00000135913,USP37,TN,.,.,FN,.,.,FN,.,.,TN,.,.,FN,.,. ENSG00000135917,SLC19A3,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000135929,CYP27A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000135940,COX5B,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000 +ENSG00000135940,COX5B,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,-0.000000 ENSG00000136003,ISCU,FN,.,.,FN,.,.,FN,.,.,FN,.,.,FN,.,. ENSG00000136010,ALDH1L2,TN,.,.,FP->TN,BS,1.000000,FP->TN,BS,1.000000,TN,,1.000000,TN,.,. ENSG00000136014,USP44,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1333,14 +1332,14 @@ ENSG00000137868,STRA6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000137869,CYP19A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000137944,KYAT3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000137968,SLC44A5,TN,,1.000000,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. -ENSG00000137992,DBT,TN,,0.999952,TN,,0.999704,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999704 +ENSG00000137992,DBT,TN,,0.999953,TN,,0.999669,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999669 ENSG00000137996,RTCA,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000138018,SELENOI,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000138029,HADHB,FP,GR|SU,0.000000,FP,GR|SU,0.000000,FP,GR|SU,0.000000,FP,GR|SU,0.000000,FP,GR|SU,0.000000 ENSG00000138030,KHK,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000138031,ADCY3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000138061,CYP1B1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP,GR,0.000000 -ENSG00000138074,SLC5A6,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,-0.000000 +ENSG00000138074,SLC5A6,FP,BS|GR,-0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 ENSG00000138075,ABCG5,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FN,.,. ENSG00000138079,SLC3A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000138109,CYP2C9,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 @@ -1390,7 +1389,7 @@ ENSG00000139287,TPH2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000139304,PTPRQ,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000139344,AMDHD1,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000139370,SLC15A4,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000139410,SDSL,TN,,1.000000,TN,,0.999976,TN,,0.999748,TN,,0.999981,TN,,0.999976 +ENSG00000139410,SDSL,TN,,1.000000,TN,,0.999976,TN,,0.999718,TN,,1.000000,TN,,1.000000 ENSG00000139428,MMAB,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000139433,GLTP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000139496,NUP58,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 @@ -1482,7 +1481,7 @@ ENSG00000143198,MGST3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000143199,ADCY10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000143207,COP1,TN,.,.,FN,.,.,FN,.,.,FN,.,.,TN,.,. ENSG00000143224,PPOX,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 -ENSG00000143252,SDHC,P,BS|ER|SU,1.000000,P,ER,1.000000,FP,ER,1.000000,FP,BS|ER|SU,1.000000,P,BS|ER|SU,1.000000 +ENSG00000143252,SDHC,P,ER,1.000000,P,ER,1.000000,FP,ER,1.000000,FP,BS|ER|SU,1.000000,P,BS|ER|SU,1.000000 ENSG00000143258,USP21,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000143278,F13B,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000143315,PIGM,FN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 @@ -1558,7 +1557,7 @@ ENSG00000146039,SLC17A4,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000146070,PLA2G7,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000146085,MMUT,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000146151,HMGCLL1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000146233,CYP39A1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. +ENSG00000146233,CYP39A1,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000146373,RNF217,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000146411,SLC2A12,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000146414,SHPRH,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1612,7 +1611,7 @@ ENSG00000148834,GSTO1,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1. ENSG00000149016,TUT1,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000149084,HSD17B12,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 ENSG00000149089,APIP,.,,1.000000,.,,1.000000,TN,,1.000000,TN,,1.000000,.,,1.000000 -ENSG00000149091,DGKZ,TN,,0.996583,TN,,1.000000,TN,,0.996583,TN,,0.996583,TN,,1.000000 +ENSG00000149091,DGKZ,TN,,0.996655,TN,,1.000000,TN,,0.996655,TN,,0.996655,TN,,1.000000 ENSG00000149124,GLYAT,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000149150,SLC43A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000149313,AASDHPPT,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 @@ -1661,7 +1660,7 @@ ENSG00000151729,SLC25A4,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,, ENSG00000151790,TDO2,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000 ENSG00000151883,PARP8,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000152127,MGAT5,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000152234,ATP5F1A,TP,ER,0.996911,TP,ER,0.996907,TP,ER,0.996890,TP,ER,0.996887,TP,ER,0.993707 +ENSG00000152234,ATP5F1A,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,TP,ER,0.986210 ENSG00000152254,G6PC2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000152256,PDK1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000152270,PDE3B,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,. @@ -1685,7 +1684,7 @@ ENSG00000153207,AHCTF1,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.0000 ENSG00000153253,SCN3A,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000 ENSG00000153291,SLC25A27,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000153395,LPCAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000153574,RPIA,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000,TP->FN,BS|IC,1.000000,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000 +ENSG00000153574,RPIA,FN,,1.000000,FP->TN,BS|IC,1.000000,TP->FN,BS|IC,1.000000,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000 ENSG00000153786,ZDHHC7,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000153827,TRIP12,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000153904,DDAH1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1700,9 +1699,9 @@ ENSG00000154252,GAL3ST2,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000154269,ENPP3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000154370,TRIM11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000154447,SH3RF1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000154518,ATP5MC3,FP,ER,0.996911,FP,ER,0.996907,FP,ER,0.996890,FP,ER,0.996887,FP,ER,0.993707 +ENSG00000154518,ATP5MC3,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 ENSG00000154678,PDE1C,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000 -ENSG00000154723,ATP5PF,P,ER,0.996911,P,ER,0.996907,P,ER,0.996890,P,ER,0.996887,P,ER,0.993707 +ENSG00000154723,ATP5PF,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 ENSG00000154914,USP43,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000154930,ACSS1,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000155016,CYP2U1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1730,7 +1729,7 @@ ENSG00000156136,DCK,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.00 ENSG00000156219,ART3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000156222,SLC28A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000156256,USP16,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000156411,ATP5MJ,FP,ER,0.996911,FP,ER,0.996907,FP,ER,0.996890,FP,ER,0.996887,FP,ER,0.993707 +ENSG00000156411,ATP5MJ,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 ENSG00000156413,FUT6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000156463,SH3RF2,TN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000156467,UQCRB,FP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|SU,0.000000,FP,BS|ER|GR|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000 @@ -1788,7 +1787,7 @@ ENSG00000158865,SLC5A11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000159063,ALG8,TN,,1.000000,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000159082,SYNJ1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000159131,GART,TP->FN,BS,1.000000,FP->TN,BS,1.000000,TP->FN,BS,1.000000,TP->FN,BS,1.000000,FP->TN,BS,1.000000 -ENSG00000159199,ATP5MC1,FP,ER,0.996911,FP,ER,0.996907,FP,ER,0.996890,FP,ER,0.996887,FP,ER,0.993707 +ENSG00000159199,ATP5MC1,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 ENSG00000159202,UBE2Z,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. ENSG00000159228,CBR1,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000159231,CBR3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1841,7 +1840,7 @@ ENSG00000160991,ORAI2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000161013,MGAT4B,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000161031,PGLYRP2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000161133,USP41P,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. -ENSG00000161217,PCYT1A,TP->FN,BS,0.981883,TN,,1.000000,TP->FN,BS,0.981884,TP->FN,BS,0.981884,FP->TN,BS,0.981881 +ENSG00000161217,PCYT1A,TP->FN,BS,0.982261,TN,,1.000000,TP->FN,BS,0.982262,TP->FN,BS,0.982262,FP->TN,BS,0.982261 ENSG00000161267,BDH1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000161281,COX7A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000161513,FDXR,TN,.,.,TN,.,.,FN,.,.,FN,.,.,TN,.,. @@ -1899,7 +1898,7 @@ ENSG00000163406,SLC15A2,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000163481,RNF25,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000163521,GLB1L,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000163527,STT3B,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 -ENSG00000163541,SUCLG1,FP,ER,0.998818,TP,ER,0.998818,TP,ER,0.998802,FP,ER,0.998799,FP,ER,0.998818 +ENSG00000163541,SUCLG1,FP,ER,0.998843,TP,ER,0.998843,TP,ER,0.998827,FP,ER,0.998822,FP,ER,0.998843 ENSG00000163581,SLC2A2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000163586,FABP1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000163590,PPM1L,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1991,7 +1990,7 @@ ENSG00000165475,CRYL1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000165526,RPUSD4,FN,.,.,FN,.,.,FN,.,.,FN,.,.,FN,.,. ENSG00000165591,FAAH2,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000165609,NUDT5,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000165629,ATP5F1C,TP,ER,0.996911,TP,ER,0.996907,TP,ER,0.996890,TP,ER,0.996887,FP,ER,0.993707 +ENSG00000165629,ATP5F1C,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,FP,ER,0.986210 ENSG00000165646,SLC18A2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000165671,NSD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000165672,PRDX3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2014,7 +2013,7 @@ ENSG00000166136,NDUFB8,FN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,FN,,1 ENSG00000166165,CKB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000166169,POLL,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000166183,ASPG,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000166224,SGPL1,FP->TN,BS,0.967887,TP->FN,BS,0.967888,FP->TN,BS,0.967890,FP->TN,BS,0.967889,FP->TN,BS,0.967883 +ENSG00000166224,SGPL1,FP->TN,BS,0.938823,TP->FN,BS,0.938793,FP->TN,BS,0.938826,FP->TN,BS,0.938827,FP->TN,BS,0.938784 ENSG00000166228,PCBD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000166311,SMPD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000166340,TPP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2051,7 +2050,7 @@ ENSG00000167165,UGT1A6,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.0000 ENSG00000167186,COQ7,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000167261,DPEP2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000167280,ENGASE,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000167283,ATP5MG,FP,ER,0.996911,FP,ER,0.996907,FP,ER,0.996890,FP,ER,0.996887,FP,ER,0.993707 +ENSG00000167283,ATP5MG,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 ENSG00000167311,ART5,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000167315,ACAA2,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000 ENSG00000167325,RRM1,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000 @@ -2081,7 +2080,7 @@ ENSG00000167780,SOAT2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000167792,NDUFV1,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000167815,PRDX2,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000167862,MRPL58,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. -ENSG00000167863,ATP5PD,FP,ER,0.996911,FP,ER,0.996907,FP,ER,0.996890,FP,ER,0.996887,FP,ER,0.993707 +ENSG00000167863,ATP5PD,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 ENSG00000167889,MGAT5B,TN,.,.,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000167900,TK1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000167910,CYP7A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2092,7 +2091,7 @@ ENSG00000168000,BSCL2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000168002,POLR2G,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 ENSG00000168003,SLC3A2,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000168032,ENTPD3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000168065,SLC22A11,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000 +ENSG00000168065,SLC22A11,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000168092,PAFAH1B2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000168159,RNF187,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000168237,GLYCTK,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2119,16 +2118,16 @@ ENSG00000168906,MAT2A,TP,BS|GR,0.000000,FP,GR,0.000000,FN,,1.000000,TP,GR,0.0000 ENSG00000168907,PLA2G4F,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000168918,INPP5D,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000168938,PPIC,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000169020,ATP5ME,TP,ER,0.996911,TP,ER,0.996907,TP,ER,0.996890,FP,ER,0.996887,FP,ER,0.993707 +ENSG00000169020,ATP5ME,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 ENSG00000169021,UQCRFS1,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|SU,0.000000,TP,BS|ER|GR|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000 ENSG00000169100,SLC25A6,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000169105,CHST14,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000169154,GOT1L1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000169169,CPT1C,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000169180,XPO6,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 -ENSG00000169239,CA5B,TN,,1.000000,TN,,1.000000,TN,,0.999990,TN,,1.000000,FP->TN,BS|IC,1.000000 +ENSG00000169239,CA5B,TN,,1.000000,FP->TN,BS|IC,1.000000,TN,,0.999990,FP->TN,BS|IC,0.999990,FP->TN,BS|IC,1.000000 ENSG00000169255,B3GALNT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000169299,PGM2,TN,,0.665734,TN,,0.665755,TN,,0.665734,TN,,0.665734,TN,,0.998295 +ENSG00000169299,PGM2,TN,,0.665754,TN,,0.665774,TN,,0.665754,TN,,0.665754,TN,,0.998332 ENSG00000169359,SLC33A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000169418,NPR1,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000169432,SCN9A,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000 @@ -2215,7 +2214,7 @@ ENSG00000172264,MACROD2,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000172269,DPAGT1,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000172288,CDY1,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000172292,CERS6,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000172296,SPTLC3,TN,,0.999777,TN,,0.999777,TN,,0.999777,TN,,0.999777,TN,,0.999777 +ENSG00000172296,SPTLC3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000172318,B3GALT1,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000172331,BPGM,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000172339,ALG14,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 @@ -2223,7 +2222,7 @@ ENSG00000172340,SUCLG2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1 ENSG00000172345,STARD5,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000172352,CDY1B,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000172456,FGGY,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000172461,FUT9,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 +ENSG00000172461,FUT9,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000172482,AGXT,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000172497,ACOT12,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000172508,CARNS1,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. @@ -2258,7 +2257,7 @@ ENSG00000173486,FKBP2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000173540,GMPPB,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000173597,SULT1B1,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000173598,NUDT4,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000173599,PC,FP->TN,BS|IC,1.000000,FP->TN,BS|IC,1.000000,TN,,1.000000,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000 +ENSG00000173599,PC,TN,,1.000000,FP->TN,BS|IC,1.000000,TN,,1.000000,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000 ENSG00000173610,UGT2A1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000173614,NMNAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000173627,APOBEC4,TN,.,.,TN,.,.,TN,.,.,FN,.,.,TN,.,. @@ -2267,7 +2266,7 @@ ENSG00000173660,UQCRH,FP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|SU,0.000000,FP,BS|E ENSG00000173786,CNP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000173838,MARCHF10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000173868,PHOSPHO1,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. -ENSG00000173915,ATP5MK,P,ER,0.996911,P,ER,0.996907,P,ER,0.996890,P,ER,0.996887,P,ER,0.993707 +ENSG00000173915,ATP5MK,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 ENSG00000173926,MARCHF3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000174080,CTSF,TN,,1.000000,TN,,1.000000,TN,.,.,FN,,1.000000,TN,,1.000000 ENSG00000174156,GSTA3,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. @@ -2282,11 +2281,11 @@ ENSG00000174473,GALNTL6,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000174502,SLC26A9,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000174607,UGT8,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000174640,SLCO2A1,TN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000,TN,.,. -ENSG00000174669,SLC29A2,TN,,0.661211,TN,,0.991688,TN,,0.991688,FN,,0.991688,TN,,0.991687 +ENSG00000174669,SLC29A2,TN,,0.661326,TN,,0.991864,TN,,0.991863,FN,,0.991863,TN,,0.991863 ENSG00000174684,B4GAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000174876,AMY1B,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000174886,NDUFA11,FN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000174915,PTDSS2,TN,,0.999999,TN,,0.999999,TN,,0.999999,TN,,0.999999,TN,,0.999999 +ENSG00000174915,PTDSS2,TN,,0.999781,TN,,0.999781,TN,,0.999781,TN,,0.999781,TN,,0.999781 ENSG00000174951,FUT1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000174990,CA5A,.,.,.,.,.,.,TN,.,.,TN,.,.,.,.,. ENSG00000175003,SLC22A1,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 @@ -2334,7 +2333,6 @@ ENSG00000176974,SHMT1,FP,BS|GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.00 ENSG00000177000,MTHFR,FP->TN,BS,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000177054,ZDHHC13,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000177076,ACER2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 -ENSG00000177084,POLE,FN,.,.,TN,.,.,FN,.,.,TN,.,.,FN,.,. ENSG00000177108,ZDHHC22,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000177156,TALDO1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000177191,B3GNT8,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -2354,7 +2352,7 @@ ENSG00000178127,NDUFV2,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1 ENSG00000178234,GALNT11,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000178301,AQP11,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000178445,GLDC,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP->TN,BS,1.000000,TN,,1.000000 -ENSG00000178537,SLC25A20,FP,BS|GR|SU,0.000000,FP,BS|GR|SU,0.000000,FP,BS|GR|SU,0.000000,FP,BS|GR|SU,0.000000,FP,BS|GR|SU,0.000000 +ENSG00000178537,SLC25A20,FP->TN,BS|SU,0.978211,FP->TN,BS|SU,0.978213,FP,BS|GR|SU,0.000000,TN,,0.978267,FP,BS|GR|SU,0.000000 ENSG00000178685,PARP10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000178700,DHFR2,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000178741,COX5A,FP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000 @@ -2379,12 +2377,12 @@ ENSG00000179913,B3GNT3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1 ENSG00000179918,SEPHS2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000179958,DCTPP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000180011,PTGR3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000180176,TH,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,FN,.,. +ENSG00000180176,TH,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FN,.,. ENSG00000180185,FAHD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000180210,F2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000180233,ZNRF2,.,.,.,.,.,.,FN,.,.,TN,.,.,.,.,. ENSG00000180251,SLC9A4,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000180389,ATP5F1EP2,P,ER,0.996911,P,ER,0.996907,P,ER,0.996890,P,ER,0.996887,P,ER,0.993707 +ENSG00000180389,ATP5F1EP2,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 ENSG00000180432,CYP8B1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000180537,RNF182,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000180549,FUT7,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -2471,7 +2469,7 @@ ENSG00000184788,SATL1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000184860,SDR42E1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000184979,USP18,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000184983,NDUFA6,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000184999,SLC22A10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. +ENSG00000184999,SLC22A10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000 ENSG00000185000,DGAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000185013,NT5C1B,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000185015,CA13,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,FP,BS|GR,0.000000 @@ -2598,7 +2596,7 @@ ENSG00000197253,TPSB2,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000197296,FITM2,FN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000197323,TRIM33,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000197355,UAP1L1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000197375,SLC22A5,TN,,0.978662,TN,,0.978663,TN,,0.978686,TN,,0.978666,TN,,0.978655 +ENSG00000197375,SLC22A5,TN,,0.999918,TN,,1.000000,TN,,0.999918,TN,,0.999918,TN,,1.000000 ENSG00000197406,DIO3,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000197408,CYP2B6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000197416,FABP12,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. @@ -2658,13 +2656,13 @@ ENSG00000198712,MT-CO2,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS| ENSG00000198721,ECI2,TN,,1.000000,FP->TN,BS|SU,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000198727,MT-CYB,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|SU,0.000000,P,BS|ER|GR|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000 ENSG00000198742,SMURF1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000198743,SLC5A3,FP->TN,SU,0.999749,FP->TN,SU,0.999749,TN,,1.000000,TN,,1.000000,FP->TN,SU,0.999749 +ENSG00000198743,SLC5A3,FP->TN,SU,0.999754,FP->TN,SU,0.999754,TN,,1.000000,TN,,1.000000,FP->TN,SU,0.999754 ENSG00000198754,OXCT2,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000198756,COLGALT2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000198763,MT-ND2,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000198786,MT-ND5,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000198804,MT-CO1,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000 -ENSG00000198805,PNP,TN,,0.998296,TN,,0.998326,TN,,0.998296,TN,,0.998296,TN,,0.998295 +ENSG00000198805,PNP,TN,,0.998332,TN,,0.998362,TN,,0.998332,TN,,0.998332,TN,,0.998332 ENSG00000198814,GK,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000198825,INPP5F,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000198833,UBE2J1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -2674,7 +2672,7 @@ ENSG00000198848,CES1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000198881,ASB12,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000198886,MT-ND4,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000198888,MT-ND1,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 -ENSG00000198899,MT-ATP6,P,ER,0.996911,P,ER,0.996907,P,ER,0.996890,P,ER,0.996887,P,ER,0.993707 +ENSG00000198899,MT-ATP6,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 ENSG00000198919,DZIP3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000198931,APRT,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000198938,MT-CO3,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000 @@ -2695,7 +2693,7 @@ ENSG00000204227,RING1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000204228,HSD17B8,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000204308,RNF5,TN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000204310,AGPAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000204370,SDHD,TP,BS|ER|SU,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 +ENSG00000204370,SDHD,TP,ER,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 ENSG00000204371,EHMT2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000204385,SLC44A4,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000204386,NEU1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2722,7 +2720,7 @@ ENSG00000213160,KLHL23,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1 ENSG00000213316,LTC4S,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000213339,QTRT1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000213366,GSTM2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000213398,LCAT,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 +ENSG00000213398,LCAT,TN,,1.000000,TN,,0.999959,TN,,1.000000,TN,,1.000000,TN,,0.999959 ENSG00000213614,HEXA,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000213619,NDUFS3,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000213648,SULT1A4,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 @@ -2751,7 +2749,7 @@ ENSG00000225697,SLC26A6,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,, ENSG00000226784,PGAM4,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000227140,USP17L5,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000227471,AKR1B15,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. -ENSG00000228253,MT-ATP8,P,ER,0.996911,P,ER,0.996907,P,ER,0.996890,P,ER,0.996887,P,ER,0.993707 +ENSG00000228253,MT-ATP8,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 ENSG00000228716,DHFR,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000228856,USP17L30,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000229579,USP17L26,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. @@ -2786,11 +2784,11 @@ ENSG00000240972,MIF,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000241119,UGT1A9,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000241360,PDXP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000241404,EGFL8,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 -ENSG00000241468,ATP5MF,FP,ER,0.996911,FP,ER,0.996907,FP,ER,0.996890,FP,ER,0.996887,FP,ER,0.993707 +ENSG00000241468,ATP5MF,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 ENSG00000241635,UGT1A1,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000241644,INMT,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000241837,ATP5PO,P,ER,0.996911,P,ER,0.996907,TP,ER,0.996890,TP,ER,0.996887,P,ER,0.993707 -ENSG00000241878,PISD,FP->TN,BS,0.999308,TN,,0.999308,FN,,0.999308,FN,,0.999308,FN,,0.999308 +ENSG00000241837,ATP5PO,P,ER,0.989294,P,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,P,ER,0.986210 +ENSG00000241878,PISD,FP->TN,BS,0.997079,TN,,0.997079,FN,,0.999105,FN,,0.997079,FN,,0.997079 ENSG00000241935,HOGA1,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP,GR,0.000000,TN,,1.000000 ENSG00000241973,PI4KA,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000242110,AMACR,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 @@ -2811,10 +2809,10 @@ ENSG00000244474,UGT1A4,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.0000 ENSG00000244486,SCARF2,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000247626,MARS2,FN,.,.,FN,.,.,FN,.,.,FN,.,.,TN,.,. ENSG00000247746,USP51,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000248098,BCKDHA,TN,,0.999952,TN,,0.999704,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999704 +ENSG00000248098,BCKDHA,TN,,0.999953,TN,,0.999669,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999669 ENSG00000248144,ADH1C,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000248933,USP17L22,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. -ENSG00000249222,ATP5MGL,P,ER,0.996911,P,ER,0.996907,TP,ER,0.996890,FP,ER,0.996887,P,ER,0.993707 +ENSG00000249222,ATP5MGL,P,ER,0.989294,P,ER,0.958110,TP,ER,0.989274,FP,ER,0.989278,P,ER,0.986210 ENSG00000249853,HS3ST5,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000249948,GBA3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000250565,ATP6V1E2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 diff --git a/data/testResults/gene-essential_summary.md b/data/testResults/gene-essential_summary.md index 5a73b0b7a..b75c2dce8 100644 --- a/data/testResults/gene-essential_summary.md +++ b/data/testResults/gene-essential_summary.md @@ -1,31 +1,32 @@ ### Graded gene essentiality vs Hart 2015 (task-scope analysis) -Run: pull request #1181, 2026-11-01. +Run: pull request #1184, 2026-11-01. Scored over every model gene that Hart 2015 scored in the cell line (`genes`); a gene outside the cell line's context model counts as non-essential, with growth ratio 1.0. The `all` row: essential in every cell line against a fitness gene in every cell line, over the genes Hart scored in every cell line (Human1 used every Hart gene). | cellLine | genes | allTaskMCC | allTaskFP | viabilityMCC | viabilityFP | growthAUROC | growthAUPRC | baseRate | capabilityOnly | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | -| DLD1 | 2654 | 0.339 | 136 | 0.3591 | 102 | 0.6452 | 0.2659 | 0.1266 | 42 | -| GBM | 2654 | 0.2947 | 139 | 0.314 | 109 | 0.6256 | 0.2444 | 0.1319 | 36 | -| HCT116 | 2714 | 0.3571 | 126 | 0.3514 | 107 | 0.645 | 0.2761 | 0.14 | 31 | -| HELA | 2716 | 0.311 | 164 | 0.3021 | 139 | 0.6453 | 0.2244 | 0.1105 | 37 | -| RPE1 | 2654 | 0.2301 | 171 | 0.2593 | 136 | 0.6197 | 0.1978 | 0.1093 | 37 | -| all | 2651 | 0.3027 | 173 | 0.3231 | 146 | 0.6363 | 0.2414 | 0.1237 | | +| DLD1 | 2652 | 0.3427 | 134 | 0.3632 | 100 | 0.644 | 0.2653 | 0.1259 | 42 | +| GBM | 2652 | 0.2905 | 141 | 0.3118 | 109 | 0.6235 | 0.2419 | 0.1316 | 38 | +| HCT116 | 2712 | 0.3585 | 126 | 0.3527 | 107 | 0.6451 | 0.2758 | 0.1394 | 31 | +| HELA | 2714 | 0.3118 | 164 | 0.3038 | 138 | 0.6433 | 0.2234 | 0.1102 | 38 | +| RPE1 | 2652 | 0.2315 | 171 | 0.2607 | 136 | 0.6183 | 0.1963 | 0.1086 | 37 | +| all | 2649 | 0.307 | 170 | 0.3269 | 144 | 0.635 | 0.2401 | 0.1232 | | ### Run environment - cobra 0.32.1, gurobipy 13.0.3, optlang 1.9.1, python 3.11.17, raven-toolbox 3.0.0b1, raven-toolbox commit ee0f8868bcc4a6f907913151a1e54dcbb4f2a160 ftINIT steps that kept an unproven incumbent (time limit or unconverged tie-break): +- HELA (reaction order 0): 1 warning(s) - RPE1 (reaction order 0): 1 warning(s) ### Gene essentiality: effect of this change (vs `develop`) -Checked **7** gene(s) directly affected plus **51** more that share a metabolite with one of them. +Checked **50** gene(s) directly affected plus **1839** more that share a metabolite with one of them. -**Likely noise** (1 gene(s), <3/5 lines): RDH5. +**Likely noise** (5 gene(s), <3/5 lines): CA5B, KL, MTHFD1, PC, RDH5. -**No change:** 57 gene(s). +**No change:** 1884 gene(s). Full per-gene, per-line detail (every gene checked, not just the ones named above): [gene-essential-diff.csv](gene-essential-diff.csv). From d1eba942c3e59d8e2b8f68e808449eb2a0a8e11b Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun, 1 Nov 2026 18:04:50 +0000 Subject: [PATCH 44/44] chore: add gene essentiality test result [skip ci] --- data/testResults/gene-essential-diff.csv | 138 +++++++++--------- data/testResults/gene-essential.csv | 160 ++++++++++----------- data/testResults/gene-essential_summary.md | 22 +-- 3 files changed, 156 insertions(+), 164 deletions(-) diff --git a/data/testResults/gene-essential-diff.csv b/data/testResults/gene-essential-diff.csv index 742e26397..a81249bb3 100644 --- a/data/testResults/gene-essential-diff.csv +++ b/data/testResults/gene-essential-diff.csv @@ -18,6 +18,7 @@ ENSG00000130377,ACSBG2,direct,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000130649,CYP2E1,direct,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000133835,HSD17B4,direct,stable,,stable,,n/a,,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000 ENSG00000134716,CYP2J2,direct,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,,,.,.,, +ENSG00000136960,ENPP2,direct,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000138061,CYP1B1,direct,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,GR,GR,0.000000,0.000000 ENSG00000138109,CYP2C9,direct,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000138115,CYP2C8,direct,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -57,7 +58,6 @@ ENSG00000002549,LAP3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00000 ENSG00000002726,AOC1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000003137,CYP26B1,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000003987,MTMR7,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000003989,SLC7A2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000004468,CD38,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,, ENSG00000004779,NDUFAB1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000004799,PDK4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, @@ -103,7 +103,6 @@ ENSG00000018280,SLC11A1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,., ENSG00000018510,AGPS,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000018625,ATP1A2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000019186,CYP24A1,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 -ENSG00000021488,SLC7A9,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000021826,CPS1,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000023228,NDUFS1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000023330,ALAS1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -116,9 +115,9 @@ ENSG00000027847,B4GALT7,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00 ENSG00000032444,PNPLA6,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000033011,ALG1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000033627,ATP6V0A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000035687,ADSS2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,BS|GR,BS|GR,0.000000,0.000000 +ENSG00000035687,ADSS2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,BS|GR,BS|GR,0.000000,-0.000000 ENSG00000036473,OTC,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000036530,CYP46A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,.,1.000000,,,,1.000000,1.000000,.,.,, +ENSG00000036530,CYP46A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000036565,SLC18A1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000036672,USP2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000038002,AGA,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -132,7 +131,7 @@ ENSG00000048028,USP28,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,., ENSG00000048392,RRM2B,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 ENSG00000049239,H6PD,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000049860,HEXB,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000050438,SLC4A8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,0.968499,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000 +ENSG00000050438,SLC4A8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,0.968497,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000 ENSG00000051382,PIK3CB,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000052802,MSMO1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000054148,PHPT1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -150,7 +149,7 @@ ENSG00000059573,ALDH18A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.0 ENSG00000060642,PIGV,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000060762,MPC1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,,,1.000000,1.000000 ENSG00000060971,ACAA1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000062485,CS,neighbor,stable,,stable,,n/a,,BS|ER|IC|SU,BS|ER|IC,1.000000,1.000000,BS|ER|IC,BS|ER|IC,1.000000,1.000000,ER|IC,ER|IC,1.000000,1.000000,BS|ER|IC|SU,BS|ER|IC|SU,1.000000,1.000000,BS|ER|IC|SU,BS|ER|IC|SU,1.000000,1.000000 +ENSG00000062485,CS,neighbor,stable,,stable,,n/a,,BS|ER|IC|SU,BS|ER|IC|SU,1.000000,1.000000,BS|ER|IC,BS|ER|IC,1.000000,1.000000,ER|IC,ER|IC,1.000000,1.000000,BS|ER|IC|SU,BS|ER|IC|SU,1.000000,1.000000,BS|ER|IC|SU,BS|ER|IC|SU,1.000000,1.000000 ENSG00000063176,SPHK2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000063601,MTMR1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000063854,HAGH,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -169,7 +168,7 @@ ENSG00000065989,PDE4A,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,,, ENSG00000066230,SLC9A3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000066322,ELOVL1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000066651,TRMT11,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000066926,FECH,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,GR,GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 +ENSG00000066926,FECH,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 ENSG00000067057,PFKP,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000067113,PLPP1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000067225,PKM,neighbor,stable,,stable,,n/a,,,,0.666699,0.666698,,,0.666699,0.666698,,,0.666699,0.666698,,,0.666699,0.666698,,,0.500024,0.500024 @@ -235,7 +234,7 @@ ENSG00000080819,CPOX,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000 ENSG00000081479,LRP2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000081923,ATP8B1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000 ENSG00000082212,ME2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000083123,BCKDHB,neighbor,stable,,stable,,n/a,,,,0.999952,0.999953,,,0.999704,0.999669,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,,,0.999704,0.999669 +ENSG00000083123,BCKDHB,neighbor,stable,,stable,,n/a,,,,0.999952,0.999953,,,0.999704,0.999710,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,,,0.999704,0.999710 ENSG00000083168,KAT6A,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000083444,PLOD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000083799,CYLD,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -246,7 +245,7 @@ ENSG00000084207,GSTP1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.0000 ENSG00000084674,APOB,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000084676,NCOA1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000084754,HADHA,neighbor,stable,,stable,,n/a,,BS|GR|SU,BS|GR|SU,0.000000,0.000000,BS|GR|SU,BS|GR|SU,0.000000,0.000000,BS|GR|SU,BS|GR|SU,0.000000,0.000000,BS|GR|SU,BS|GR|SU,0.000000,0.000000,BS|GR|SU,BS|GR|SU,0.000000,0.000000 -ENSG00000084774,CAD,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 +ENSG00000084774,CAD,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,-0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 ENSG00000085377,PREP,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000085563,ABCB1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000085662,AKR1B1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -281,8 +280,8 @@ ENSG00000090402,SI,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,,,1.000000,1. ENSG00000090661,CERS4,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,, ENSG00000090686,USP48,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000090971,NAT14,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000091140,DLD,neighbor,stable,,stable,,n/a,,ER,ER,0.996886,0.989270,ER,ER,0.996573,0.988929,ER|GR,ER|GR,0.000000,0.000000,BS|ER|GR,BS|ER|GR,0.000000,0.000000,BS|ER|IC|SU,BS|ER|IC|SU,0.996573,0.988928 -ENSG00000091483,FH,neighbor,stable,,stable,,n/a,,BS|ER|GR|SU,BS|ER,-0.000000,1.000000,BS|ER,BS|ER,1.000000,1.000000,BS|ER,BS|ER,1.000000,1.000000,BS|ER|SU,BS|ER|SU,1.000000,1.000000,BS|ER|SU,BS|ER|SU,1.000000,1.000000 +ENSG00000091140,DLD,neighbor,stable,,stable,,n/a,,ER,ER,0.996886,0.989270,ER,ER,0.996573,0.988969,ER|GR,ER|GR,0.000000,0.000000,BS|ER|GR,BS|ER|GR,0.000000,0.000000,BS|ER|IC|SU,BS|ER|IC|SU,0.996573,0.988967 +ENSG00000091483,FH,neighbor,stable,,stable,,n/a,,BS|ER|GR|SU,BS|ER|SU,-0.000000,1.000000,BS|ER,BS|ER,1.000000,1.000000,BS|ER,BS|ER,1.000000,1.000000,BS|ER|SU,BS|ER|SU,1.000000,1.000000,BS|ER|SU,BS|ER|SU,1.000000,1.000000 ENSG00000091664,SLC17A6,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000091704,CPA1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000092009,CMA1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -293,7 +292,7 @@ ENSG00000093217,XYLB,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00000 ENSG00000094963,FMO2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000095059,DHPS,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000095303,PTGS1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, -ENSG00000095321,CRAT,neighbor,stable,,stable,,n/a,,BS|SU,BS|SU,0.978662,0.999918,BS|SU,BS|SU,0.978663,1.000000,BS|SU,BS|SU,0.978686,0.999918,BS|SU,BS|SU,0.978666,0.999918,BS|SU,BS|SU,0.978655,1.000000 +ENSG00000095321,CRAT,neighbor,stable,,stable,,n/a,,BS|SU,BS|SU,0.978662,0.999918,BS|SU,BS|SU,0.978663,0.999918,BS|SU,BS|SU,0.978686,0.999918,BS|SU,BS|SU,0.978666,1.000000,BS|SU,BS|SU,0.978655,0.999918 ENSG00000095380,NANS,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000095464,PDE6C,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000095596,CYP26A1,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 @@ -303,9 +302,9 @@ ENSG00000097033,SH3GLB1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,., ENSG00000099194,SCD,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000099377,HSD3B7,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000099381,SETD1A,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000099624,ATP5F1D,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000099624,ATP5F1D,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000099795,NDUFB7,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000099797,TECR,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 +ENSG00000099797,TECR,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,-0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000099904,ZDHHC8,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000099998,GGT5,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,, ENSG00000100024,UPB1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -326,7 +325,7 @@ ENSG00000100292,HMOX1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.0000 ENSG00000100299,ARSA,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000100344,PNPLA3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000100348,TXN2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000100372,SLC25A17,neighbor,stable,,stable,,n/a,,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000 +ENSG00000100372,SLC25A17,neighbor,isolated (likely noise),1/5,stable,,n/a,,BS|SU,BS|SU,1.000000,1.000000,BS|SU,,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000 ENSG00000100393,EP300,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000100416,TRMU,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000100422,CERK,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -338,7 +337,7 @@ ENSG00000100577,GSTZ1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.0000 ENSG00000100596,SPTLC2,neighbor,stable,,stable,,n/a,,,,0.999777,1.000000,,,0.999777,1.000000,,,0.999777,1.000000,,,0.999777,1.000000,,,0.999777,1.000000 ENSG00000100600,LGMN,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000100605,ITPK1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000100714,MTHFD1,neighbor,isolated (likely noise),1/5,stable,,n/a,,,BS,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000100714,MTHFD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000100867,DHRS2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,, ENSG00000100938,GMPR2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000100983,GSS,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 @@ -375,7 +374,7 @@ ENSG00000102575,ACP5,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,.,. ENSG00000102699,PARP4,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000102743,SLC25A15,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000102780,DGKH,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000102794,ACOD1,neighbor,stable,,stable,,n/a,,,.,1.000000,,,.,1.000000,,,,1.000000,1.000000,.,.,,,,.,1.000000, +ENSG00000102794,ACOD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000 ENSG00000103044,HAS3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000103056,SMPD3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,, ENSG00000103064,SLC7A6,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -385,7 +384,6 @@ ENSG00000103174,NAGPA,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,., ENSG00000103194,USP10,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000103222,ABCC1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000103253,HAGHL,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000103257,SLC7A5,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000103375,AQP8,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000103404,USP31,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000103415,HMOX2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -415,7 +413,7 @@ ENSG00000104812,GYS1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00000 ENSG00000104823,ECH1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000104879,CKM,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000104885,DOT1L,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000104888,SLC17A7,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,0.999890,.,.,,,.,.,, +ENSG00000104888,SLC17A7,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,, ENSG00000104907,TRMT1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000104951,IL4I1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,.,.,, ENSG00000105143,SLC1A6,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -504,7 +502,7 @@ ENSG00000110871,COQ5,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR ENSG00000110887,DAO,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000110911,SLC11A2,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,,,1.000000,1.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,,,1.000000,1.000000 ENSG00000110921,MVK,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 -ENSG00000110955,ATP5F1B,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000110955,ATP5F1B,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000111012,CYP27B1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000111058,ACSS3,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,,,,,1.000000,1.000000 ENSG00000111077,TNS2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -514,7 +512,7 @@ ENSG00000111261,MANSC1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000 ENSG00000111275,ALDH2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000111339,ART4,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000111371,SLC38A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000111640,GAPDH,neighbor,stable,,stable,,n/a,,,,0.501952,0.501911,,,0.557725,0.557690,,,0.557725,0.557678,,,1.000000,1.000000,,,0.500000,0.500000 +ENSG00000111640,GAPDH,neighbor,stable,,stable,,n/a,,,,0.501952,0.501911,,,0.557725,0.557678,,,0.557725,0.557678,,,1.000000,1.000000,,,0.500000,0.500000 ENSG00000111666,CHPT1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000111667,USP5,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000111674,ENO2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -552,7 +550,6 @@ ENSG00000113396,SLC27A6,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.0 ENSG00000113448,PDE4D,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,.,.,, ENSG00000113456,RAD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000113552,GNPDA1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000113643,RARS1,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 ENSG00000113732,ATP6V0E1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000113790,EHHADH,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000113924,HGD,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -599,7 +596,7 @@ ENSG00000116157,GPX7,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,.,. ENSG00000116199,FAM20B,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000116337,AMPD2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000116353,MECR,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,0.999997,0.999990,,,1.000000,1.000000 -ENSG00000116459,ATP5PB,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000116459,ATP5PB,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000116539,ASH1L,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000116649,SRM,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000116711,PLA2G4A,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -661,7 +658,7 @@ ENSG00000120265,PCMT1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,., ENSG00000120329,SLC25A2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,,,1.000000,1.000000 ENSG00000120437,ACAT2,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS,BS,0.994466,0.994583,BS,BS,0.994466,0.994583,BS|GR,BS|GR,0.000000,0.000000 ENSG00000120563,LYZL1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000120697,ALG5,neighbor,stable,,stable,,n/a,,,,1.000000,0.999992,,,1.000000,0.999992,,,1.000000,1.000000,,,1.000000,0.999991,,,1.000000,0.999990 +ENSG00000120697,ALG5,neighbor,stable,,stable,,n/a,,,,1.000000,0.999992,,,1.000000,0.999992,,,1.000000,1.000000,,,1.000000,0.999991,,,1.000000,0.999991 ENSG00000120820,GLT8D2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000120915,EPHX2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000120992,LYPLA1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -687,12 +684,12 @@ ENSG00000123453,SARDH,neighbor,stable,,stable,,n/a,,BS,BS,1.000000,1.000000,.,., ENSG00000123454,DBH,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000123505,AMD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000123552,USP45,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000123643,SLC36A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,BS,BS,1.000000,1.000000,,,1.000000,1.000000,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000 +ENSG00000123643,SLC36A1,neighbor,stable,,isolated (likely noise),1/5,regression,,,,1.000000,1.000000,BS,BS,1.000000,1.000000,,,1.000000,1.000000,BS,BS|GR,1.000000,0.000000,BS,BS,1.000000,1.000000 ENSG00000123739,PLA2G12A,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000123836,PFKFB2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000124091,GCNT7,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,, ENSG00000124151,NCOA3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000124172,ATP5F1E,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000124172,ATP5F1E,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000124181,PLCG1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000124275,MTRR,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000124299,PEPD,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -720,11 +717,10 @@ ENSG00000125877,ITPA,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00000 ENSG00000126088,UROD,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 ENSG00000126267,COX6B1,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,,,1.000000,1.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 ENSG00000126432,PRDX5,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000126522,ASL,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000126821,SGPP1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000127080,IPPK,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000127125,PPCS,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,-0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 -ENSG00000127184,COX7C,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 +ENSG00000127125,PPCS,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,-0.000000 +ENSG00000127184,COX7C,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,-0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 ENSG00000127415,IDUA,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000127472,PLA2G5,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000127540,UQCR11,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 @@ -818,7 +814,7 @@ ENSG00000132958,TPTE2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.0000 ENSG00000133027,PEMT,neighbor,stable,,stable,,n/a,,BS,BS,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000133056,PIK3C2B,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000133063,CHIT1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000133116,KL,neighbor,isolated (likely noise),1/1,isolated (likely noise),1/1,regression,,.,.,,,.,.,,,.,.,,,.,.,,,.,GR,,0.000000 +ENSG00000133116,KL,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000133247,KMT5C,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000133256,PDE6B,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000133313,CNDP2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -855,9 +851,9 @@ ENSG00000135220,UGT2A3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,, ENSG00000135226,UGT2B28,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000135241,PNPLA8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000135318,NT5E,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000135390,ATP5MC2,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000135390,ATP5MC2,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000135423,GLS2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,.,.,, -ENSG00000135437,RDH5,neighbor,isolated (likely noise),2/5,isolated (likely noise),2/5,mixed,,GR,,0.000000,1.000000,GR,,0.000000,1.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 +ENSG00000135437,RDH5,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000135454,B4GALNT1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000135587,SMPD2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000135655,USP15,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -870,7 +866,7 @@ ENSG00000135845,PIGC,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00000 ENSG00000135913,USP37,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000135917,SLC19A3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000135929,CYP27A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000135940,COX5B,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,-0.000000 +ENSG00000135940,COX5B,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 ENSG00000136003,ISCU,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000136010,ALDH1L2,neighbor,stable,,stable,,n/a,,.,.,,,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000136014,USP44,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -884,20 +880,19 @@ ENSG00000136699,SMPD4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.0000 ENSG00000136750,GAD2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000136810,TXN,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000136840,ST6GALNAC4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000136877,FPGS,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,BS,BS,1.000000,1.000000,,,1.000000,1.000000,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000 +ENSG00000136877,FPGS,neighbor,stable,,isolated (likely noise),1/5,improvement,,,,1.000000,1.000000,BS,BS,1.000000,1.000000,,,1.000000,1.000000,BS,BS|GR,1.000000,0.000000,BS,BS,1.000000,1.000000 ENSG00000136878,USP20,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000136881,BAAT,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000136888,ATP6V1G1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000136908,DPM2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000136943,CTSV,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000136960,ENPP2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000137106,GRHPR,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000137124,ALDH1B1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000137198,GMPR,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000 ENSG00000137200,CMTR1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000137364,TPMT,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000137491,SLCO2B1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000137563,GGH,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,BS,BS,1.000000,1.000000,,,1.000000,1.000000,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000 +ENSG00000137563,GGH,neighbor,stable,,isolated (likely noise),1/5,regression,,,,1.000000,1.000000,BS,BS,1.000000,1.000000,,,1.000000,1.000000,BS,BS|GR,1.000000,0.000000,BS,BS,1.000000,1.000000 ENSG00000137714,FDX1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000137731,FXYD2,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,, ENSG00000137767,SQOR,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -912,7 +907,6 @@ ENSG00000138018,SELENOI,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00 ENSG00000138029,HADHB,neighbor,stable,,stable,,n/a,,GR|SU,GR|SU,0.000000,0.000000,GR|SU,GR|SU,0.000000,0.000000,GR|SU,GR|SU,0.000000,0.000000,GR|SU,GR|SU,0.000000,0.000000,GR|SU,GR|SU,0.000000,0.000000 ENSG00000138030,KHK,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000138075,ABCG5,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000138079,SLC3A1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000138134,STAMBPL1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000138135,CH25H,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,, ENSG00000138185,ENTPD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -946,10 +940,9 @@ ENSG00000139287,TPH2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000139304,PTPRQ,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000139344,AMDHD1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,, ENSG00000139370,SLC15A4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000139410,SDSL,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,0.999976,0.999976,,,0.999748,0.999718,,,0.999981,1.000000,,,0.999976,1.000000 +ENSG00000139410,SDSL,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,0.999976,0.999976,,,0.999748,0.999753,,,0.999981,0.999981,,,0.999976,1.000000 ENSG00000139428,MMAB,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000139505,MTMR6,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000139514,SLC7A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000139531,SUOX,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000139540,SLC39A5,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000139547,RDH16,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -1046,10 +1039,9 @@ ENSG00000145626,UGT3A1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,. ENSG00000145675,PIK3R1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000145725,PPIP5K2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000145730,PAM,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000146233,CYP39A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,.,1.000000,,,,1.000000,1.000000,.,.,, +ENSG00000146233,CYP39A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000146701,MDH2,neighbor,stable,,stable,,n/a,,ER,ER,1.000000,1.000000,ER,ER,1.000000,1.000000,ER,ER,1.000000,1.000000,ER,ER,1.000000,1.000000,ER,ER,1.000000,1.000000 ENSG00000146733,PSPH,neighbor,stable,,stable,,n/a,,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000 -ENSG00000147003,CLTRN,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000147119,CHST7,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000147123,NDUFB11,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000147224,PRPS1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1074,7 +1066,7 @@ ENSG00000148832,PAOX,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,,,1 ENSG00000148834,GSTO1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000149084,HSD17B12,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000149089,APIP,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000149091,DGKZ,neighbor,stable,,stable,,n/a,,,,0.996583,0.996655,,,1.000000,1.000000,,,0.996583,0.996655,,,0.996583,0.996655,,,1.000000,1.000000 +ENSG00000149091,DGKZ,neighbor,stable,,stable,,n/a,,,,0.996583,0.996655,,,1.000000,1.000000,,,0.996583,0.996655,,,0.996583,0.996615,,,1.000000,1.000000 ENSG00000149124,GLYAT,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000149313,AASDHPPT,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000149380,P4HA3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, @@ -1102,7 +1094,7 @@ ENSG00000151632,AKR1C2,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,. ENSG00000151689,INPP1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000151790,TDO2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,.,.,,,,,1.000000,1.000000 ENSG00000151883,PARP8,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000152234,ATP5F1A,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000152234,ATP5F1A,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000152254,G6PC2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000152256,PDK1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000152270,PDE3B,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, @@ -1125,9 +1117,9 @@ ENSG00000154080,CHST9,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,., ENSG00000154227,CERS3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000154252,GAL3ST2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000154269,ENPP3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000154518,ATP5MC3,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000154518,ATP5MC3,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000154678,PDE1C,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000154723,ATP5PF,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000154723,ATP5PF,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000154914,USP43,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000154930,ACSS1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,.,.,,,.,.,, ENSG00000155016,CYP2U1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1145,7 +1137,7 @@ ENSG00000156110,ADK,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000 ENSG00000156136,DCK,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000156219,ART3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000156256,USP16,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000156411,ATP5MJ,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000156411,ATP5MJ,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000156413,FUT6,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000156467,UQCRB,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 ENSG00000156510,HKDC1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,,,1.000000,1.000000 @@ -1185,7 +1177,7 @@ ENSG00000158864,NDUFS2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000 ENSG00000159063,ALG8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000159082,SYNJ1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000159131,GART,neighbor,stable,,stable,,n/a,,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000,BS,BS,1.000000,1.000000 -ENSG00000159199,ATP5MC1,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000159199,ATP5MC1,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000159228,CBR1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000159231,CBR3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000159267,HLCS,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1221,7 +1213,7 @@ ENSG00000160882,CYP11B1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,., ENSG00000160883,HK3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000161031,PGLYRP2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000161133,USP41P,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000161217,PCYT1A,neighbor,stable,,stable,,n/a,,BS,BS,0.981883,0.982261,,,1.000000,1.000000,BS,BS,0.981884,0.982262,BS,BS,0.981884,0.982262,BS,BS,0.981881,0.982261 +ENSG00000161217,PCYT1A,neighbor,stable,,stable,,n/a,,BS,BS,0.981883,0.982261,,,1.000000,1.000000,BS,BS,0.981884,0.982262,BS,BS,0.981884,0.982264,BS,BS,0.981881,0.982259 ENSG00000161267,BDH1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000161281,COX7A1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000161513,FDXR,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -1285,7 +1277,6 @@ ENSG00000164181,ELOVL7,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,, ENSG00000164258,NDUFS4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000164294,GPX8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000164303,ENPP6,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,, -ENSG00000164363,SLC6A18,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000164405,UQCRQ,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 ENSG00000164535,DAGLB,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000164638,SLC29A4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1306,14 +1297,13 @@ ENSG00000165195,PIGA,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00000 ENSG00000165264,NDUFB6,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000165269,AQP7,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000165272,AQP3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, -ENSG00000165349,SLC7A3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000165434,PGM2L1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000165458,INPPL1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000165475,CRYL1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000165526,RPUSD4,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000165591,FAAH2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000165609,NUDT5,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000165629,ATP5F1C,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000165629,ATP5F1C,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000165646,SLC18A2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000165671,NSD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000165672,PRDX3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1330,7 +1320,7 @@ ENSG00000166135,HIF1AN,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,. ENSG00000166136,NDUFB8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000166165,CKB,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000166183,ASPG,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000166224,SGPL1,neighbor,stable,,stable,,n/a,,BS,BS,0.967887,0.938823,BS,BS,0.967888,0.938793,BS,BS,0.967890,0.938826,BS,BS,0.967889,0.938827,BS,BS,0.967883,0.938784 +ENSG00000166224,SGPL1,neighbor,stable,,stable,,n/a,,BS,BS,0.967887,0.938823,BS,BS,0.967888,0.938824,BS,BS,0.967890,0.938826,BS,BS,0.967889,0.938795,BS,BS,0.967883,0.938816 ENSG00000166228,PCBD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000166311,SMPD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000166340,TPP1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1354,7 +1344,7 @@ ENSG00000167130,DOLPP1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000 ENSG00000167165,UGT1A6,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000167186,COQ7,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000167280,ENGASE,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000167283,ATP5MG,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000167283,ATP5MG,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000167311,ART5,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,, ENSG00000167315,ACAA2,neighbor,stable,,stable,,n/a,,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000 ENSG00000167325,RRM1,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 @@ -1373,7 +1363,7 @@ ENSG00000167769,ACER1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,., ENSG00000167792,NDUFV1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000167815,PRDX2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000167862,MRPL58,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000167863,ATP5PD,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000167863,ATP5PD,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000167889,MGAT5B,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000167900,TK1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000167910,CYP7A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1395,12 +1385,12 @@ ENSG00000168781,PPIP5K1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00 ENSG00000168906,MAT2A,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,GR,GR,0.000000,0.000000,,,1.000000,1.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 ENSG00000168907,PLA2G4F,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000168918,INPP5D,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,.,.,, -ENSG00000169020,ATP5ME,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000169020,ATP5ME,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000169021,UQCRFS1,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 ENSG00000169154,GOT1L1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000169169,CPT1C,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000169180,XPO6,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000169239,CA5B,neighbor,isolated (likely noise),2/5,stable,,n/a,,,,1.000000,1.000000,,BS|IC,1.000000,1.000000,,,0.999990,0.999990,,BS|IC,1.000000,0.999990,BS|IC,BS|IC,1.000000,1.000000 +ENSG00000169239,CA5B,neighbor,consensus gained,3/5,stable,,n/a,,,BS|IC,1.000000,1.000000,,BS|IC,1.000000,1.000000,,,0.999990,0.999990,,BS|IC,1.000000,0.999990,BS|IC,,1.000000,1.000000 ENSG00000169599,NFU1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000169660,HEXD,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000169710,FASN,neighbor,stable,,stable,,n/a,,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000 @@ -1446,7 +1436,6 @@ ENSG00000171560,FGA,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000171608,PIK3CD,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000171723,GPHN,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000171759,PAH,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000171766,GATM,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,.,.,,,.,.,, ENSG00000171793,CTPS1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000171848,RRM2,neighbor,stable,,stable,,n/a,,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000,BS|GR,BS|GR,0.000000,0.000000 ENSG00000171862,PTEN,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1463,9 +1452,9 @@ ENSG00000172331,BPGM,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00000 ENSG00000172339,ALG14,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000172352,CDY1B,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000172456,FGGY,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000172461,FUT9,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,,.,1.000000, +ENSG00000172461,FUT9,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000172497,ACOT12,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000172508,CARNS1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, +ENSG00000172508,CARNS1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,,,1.000000 ENSG00000172543,CTSW,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000172572,PDE3A,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,, ENSG00000172613,RAD9A,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1491,15 +1480,15 @@ ENSG00000173281,PPP1R3B,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00 ENSG00000173540,GMPPB,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000173597,SULT1B1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000173598,NUDT4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000173599,PC,neighbor,isolated (likely noise),1/5,stable,,n/a,,BS|IC,,1.000000,1.000000,BS|IC,BS|IC,1.000000,1.000000,,,1.000000,1.000000,BS|IC,BS|IC,1.000000,1.000000,BS|IC,BS|IC,1.000000,1.000000 +ENSG00000173599,PC,neighbor,stable,,stable,,n/a,,BS|IC,BS|IC,1.000000,1.000000,BS|IC,BS|IC,1.000000,1.000000,,,1.000000,1.000000,BS|IC,BS|IC,1.000000,1.000000,BS|IC,BS|IC,1.000000,1.000000 ENSG00000173610,UGT2A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000173614,NMNAT1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000173627,APOBEC4,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000173638,SLC19A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,ER,ER,1.000000,1.000000 +ENSG00000173638,SLC19A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,ER,BS|ER,1.000000,1.000000 ENSG00000173660,UQCRH,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|SU,BS|ER|GR|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 ENSG00000173786,CNP,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000173868,PHOSPHO1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, -ENSG00000173915,ATP5MK,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000173915,ATP5MK,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000174080,CTSF,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000174156,GSTA3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000174437,ATP2A2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1507,6 +1496,7 @@ ENSG00000174607,UGT8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1 ENSG00000174684,B4GAT1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000174876,AMY1B,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000174886,NDUFA11,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000174915,PTDSS2,neighbor,stable,,stable,,n/a,,,,0.999999,0.999781,,,0.999999,0.999781,,,0.999999,0.999781,,,0.999999,0.999781,,,0.999999,0.999781 ENSG00000174951,FUT1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000174990,CA5A,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000175048,ZDHHC14,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -1529,6 +1519,7 @@ ENSG00000176340,COX8A,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|S ENSG00000176383,B3GNT4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000176387,HSD11B2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000176393,RNPEP,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000176454,LPCAT4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000176485,PLAAT3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000176597,B3GNT5,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000176715,ACSF3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -1569,11 +1560,11 @@ ENSG00000179913,B3GNT3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000 ENSG00000179918,SEPHS2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000179958,DCTPP1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000180011,PTGR3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000180176,TH,neighbor,stable,,stable,,n/a,,.,.,,,,.,1.000000,,.,.,,,.,.,,,.,.,, +ENSG00000180176,TH,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,, ENSG00000180185,FAHD1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000180210,F2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000180251,SLC9A4,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000180389,ATP5F1EP2,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000180389,ATP5F1EP2,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000180432,CYP8B1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000180549,FUT7,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000180638,SLC47A2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -1626,7 +1617,7 @@ ENSG00000184860,SDR42E1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,, ENSG00000184979,USP18,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000184983,NDUFA6,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000185013,NT5C1B,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,.,.,,,.,.,,,.,.,, -ENSG00000185015,CA13,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,BS|GR,BS|GR,0.000000,0.000000 +ENSG00000185015,CA13,neighbor,isolated (likely noise),1/4,isolated (likely noise),1/4,improvement,,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,BS|GR,,0.000000,1.000000 ENSG00000185100,ADSS1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000185133,INPP5J,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,, ENSG00000185344,ATP6V0A2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1755,7 +1746,7 @@ ENSG00000198848,CES1,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000198881,ASB12,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000198886,MT-ND4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000198888,MT-ND1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000198899,MT-ATP6,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000198899,MT-ATP6,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000198938,MT-CO3,neighbor,stable,,stable,,n/a,,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000,BS|ER|GR|IC|SU,BS|ER|GR|IC|SU,0.000000,0.000000 ENSG00000198951,NAGA,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000203797,DDO,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 @@ -1806,7 +1797,7 @@ ENSG00000225697,SLC26A6,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00 ENSG00000226784,PGAM4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000227140,USP17L5,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000227471,AKR1B15,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000228253,MT-ATP8,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000228253,MT-ATP8,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000228716,DHFR,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000228856,USP17L30,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000229579,USP17L26,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -1833,13 +1824,13 @@ ENSG00000240891,PLCXD2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000 ENSG00000241119,UGT1A9,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000241360,PDXP,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000241404,EGFL8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000 -ENSG00000241468,ATP5MF,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000241468,ATP5MF,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000241635,UGT1A1,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000241644,INMT,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000241837,ATP5PO,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 -ENSG00000241878,PISD,neighbor,stable,,stable,,n/a,,BS,BS,0.999308,0.997079,,,0.999308,0.997079,,,0.999308,0.999105,,,0.999308,0.997079,,,0.999308,0.997079 +ENSG00000241837,ATP5PO,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 +ENSG00000241878,PISD,neighbor,stable,,stable,,n/a,,BS,BS,0.999308,0.995061,,,0.999308,0.997079,,,0.999308,0.999105,,,0.999308,0.995062,,,0.999308,0.997079 ENSG00000241973,PI4KA,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000242366,UGT1A8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 +ENSG00000242366,UGT1A8,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,0.999999 ENSG00000242515,UGT1A10,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000242612,DECR2,neighbor,stable,,stable,,n/a,,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000,BS|SU,BS|SU,1.000000,1.000000 ENSG00000243480,AMY2A,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,,,1.000000,1.000000,.,.,, @@ -1853,10 +1844,10 @@ ENSG00000244122,UGT1A7,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000 ENSG00000244474,UGT1A4,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000244486,SCARF2,neighbor,stable,,stable,,n/a,,.,.,,,,,1.000000,1.000000,,,1.000000,1.000000,.,.,,,,,1.000000,1.000000 ENSG00000247746,USP51,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000248098,BCKDHA,neighbor,stable,,stable,,n/a,,,,0.999952,0.999953,,,0.999704,0.999669,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,,,0.999704,0.999669 +ENSG00000248098,BCKDHA,neighbor,stable,,stable,,n/a,,,,0.999952,0.999953,,,0.999704,0.999710,GR,GR,0.000000,0.000000,GR,GR,0.000000,0.000000,,,0.999704,0.999710 ENSG00000248144,ADH1C,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000248933,USP17L22,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, -ENSG00000249222,ATP5MGL,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958110,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989278,ER,ER,0.993707,0.986210 +ENSG00000249222,ATP5MGL,neighbor,stable,,stable,,n/a,,ER,ER,0.996911,0.989294,ER,ER,0.996907,0.958107,ER,ER,0.996890,0.989274,ER,ER,0.996887,0.989273,ER,ER,0.993707,0.989293 ENSG00000249948,GBA3,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000250565,ATP6V1E2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000250799,PRODH2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, @@ -1874,7 +1865,6 @@ ENSG00000265203,RBP3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.00000 ENSG00000266200,PNLIPRP2,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000267673,FDX2,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, ENSG00000267855,NDUFA7,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 -ENSG00000268104,SLC6A14,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000272325,NUDT3,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000272333,KMT2B,neighbor,stable,,stable,,n/a,,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000,,,1.000000,1.000000 ENSG00000273820,USP27X,neighbor,stable,,stable,,n/a,,.,.,,,.,.,,,.,.,,,.,.,,,.,.,, diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv index bcb6e87aa..30bff1f67 100644 --- a/data/testResults/gene-essential.csv +++ b/data/testResults/gene-essential.csv @@ -115,9 +115,9 @@ ENSG00000033178,UBA6,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. ENSG00000033627,ATP6V0A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000033867,SLC4A7,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000034677,RNF19A,TN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000035687,ADSS2,.,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,FP,BS|GR,0.000000 +ENSG00000035687,ADSS2,.,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,FP,BS|GR,-0.000000 ENSG00000036473,OTC,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000036530,CYP46A1,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. +ENSG00000036530,CYP46A1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000036565,SLC18A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000036672,USP2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000037757,MRI1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -133,13 +133,13 @@ ENSG00000047230,CTPS2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000047249,ATP6V1H,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000047315,POLR2B,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 ENSG00000047410,TPR,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 -ENSG00000047457,CP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 +ENSG00000047457,CP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,0.999999 ENSG00000048028,USP28,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000048392,RRM2B,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 ENSG00000049239,H6PD,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000049759,NEDD4L,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000049860,HEXB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000050438,SLC4A8,TN,,1.000000,TN,,0.968499,TN,,1.000000,TN,.,.,TN,,1.000000 +ENSG00000050438,SLC4A8,TN,,1.000000,TN,,0.968497,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000051341,POLQ,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000051382,PIK3CB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000052802,MSMO1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -151,7 +151,7 @@ ENSG00000054983,GALC,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000055483,USP36,FN,.,.,FN,.,.,FN,.,.,TN,.,.,FN,.,. ENSG00000055609,KMT2C,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000056998,GYG2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000057252,SOAT1,TN,,0.999918,TN,,1.000000,TN,,0.999918,TN,,0.999918,TN,,1.000000 +ENSG00000057252,SOAT1,TN,,0.999918,TN,,0.999918,TN,,0.999918,TN,,1.000000,TN,,0.999918 ENSG00000058056,USP13,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000058600,POLR3E,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 ENSG00000058668,ATP2B4,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -167,7 +167,7 @@ ENSG00000060971,ACAA1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1. ENSG00000060982,BCAT1,TN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000,FN,,1.000000 ENSG00000061918,GUCY1B1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000062282,DGAT2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000062485,CS,FP,BS|ER|IC,1.000000,TP,BS|ER|IC,1.000000,FP,ER|IC,1.000000,FP,BS|ER|IC|SU,1.000000,FP,BS|ER|IC|SU,1.000000 +ENSG00000062485,CS,FP,BS|ER|IC|SU,1.000000,TP,BS|ER|IC,1.000000,FP,ER|IC,1.000000,FP,BS|ER|IC|SU,1.000000,FP,BS|ER|IC|SU,1.000000 ENSG00000062822,POLD1,FN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000063176,SPHK2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000063601,MTMR1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -194,7 +194,7 @@ ENSG00000066322,ELOVL1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1 ENSG00000066379,POLR1H,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 ENSG00000066651,TRMT11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000066813,ACSM2B,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. -ENSG00000066926,FECH,FP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,GR,0.000000,FP,BS|GR,0.000000 +ENSG00000066926,FECH,FP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 ENSG00000067057,PFKP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000067064,IDI1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000067113,PLPP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -250,7 +250,7 @@ ENSG00000072682,P4HA2,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000072778,ACADVL,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,1.000000,FP->TN,SU,1.000000 ENSG00000073060,SCARB1,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000073417,PDE8A,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000073578,SDHA,TP,ER,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,TP,BS|ER|SU,1.000000 +ENSG00000073578,SDHA,TP,BS|ER|SU,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,TP,BS|ER|SU,1.000000 ENSG00000073734,ABCB11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000073737,DHRS9,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000073756,PTGS2,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 @@ -311,7 +311,7 @@ ENSG00000081800,SLC13A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,, ENSG00000081923,ATP8B1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000082212,ME2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000082996,RNF13,.,.,.,.,.,.,TN,.,.,TN,.,.,.,.,. -ENSG00000083123,BCKDHB,TN,,0.999953,TN,,0.999669,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999669 +ENSG00000083123,BCKDHB,TN,,0.999953,TN,,0.999710,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999710 ENSG00000083168,KAT6A,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000083223,TUT7,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000083444,PLOD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 @@ -327,7 +327,7 @@ ENSG00000084453,SLCO1A2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,, ENSG00000084674,APOB,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000084676,NCOA1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000084754,HADHA,FP,BS|GR|SU,0.000000,FP,BS|GR|SU,0.000000,FP,BS|GR|SU,0.000000,FP,BS|GR|SU,0.000000,FP,BS|GR|SU,0.000000 -ENSG00000084774,CAD,TP,BS|GR,0.000000,FP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000 +ENSG00000084774,CAD,TP,BS|GR,-0.000000,FP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000 ENSG00000085231,AK6,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000085377,PREP,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000085382,HACE1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -380,8 +380,8 @@ ENSG00000090861,AARS1,TP,BS|GR,0.000000,FP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,B ENSG00000090971,NAT14,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000091137,SLC26A4,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000 ENSG00000091138,SLC26A3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000091140,DLD,TP,ER,0.989270,TP,ER,0.988929,TP,ER|GR,0.000000,FP,BS|ER|GR,0.000000,TP,BS|ER|IC|SU,0.988928 -ENSG00000091483,FH,TP,BS|ER,1.000000,FP,BS|ER,1.000000,TP,BS|ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 +ENSG00000091140,DLD,TP,ER,0.989270,TP,ER,0.988969,TP,ER|GR,0.000000,FP,BS|ER|GR,0.000000,TP,BS|ER|IC|SU,0.988967 +ENSG00000091483,FH,TP,BS|ER|SU,1.000000,FP,BS|ER,1.000000,TP,BS|ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 ENSG00000091664,SLC17A6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000091704,CPA1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000092009,CMA1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -400,7 +400,7 @@ ENSG00000095059,DHPS,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.0 ENSG00000095139,ARCN1,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000095303,PTGS1,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000095319,NUP188,TP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 -ENSG00000095321,CRAT,FP->TN,BS|SU,0.999918,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,0.999918,FP->TN,BS|SU,0.999918,FP->TN,BS|SU,1.000000 +ENSG00000095321,CRAT,FP->TN,BS|SU,0.999918,FP->TN,BS|SU,0.999918,FP->TN,BS|SU,0.999918,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,0.999918 ENSG00000095380,NANS,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000095464,PDE6C,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000095596,CYP26A1,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000 @@ -414,10 +414,10 @@ ENSG00000097033,SH3GLB1,TN,.,.,TN,.,.,TN,.,.,FN,.,.,TN,.,. ENSG00000099194,SCD,FN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000099377,HSD3B7,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000099381,SETD1A,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 -ENSG00000099624,ATP5F1D,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,TP,ER,0.986210 +ENSG00000099624,ATP5F1D,TP,ER,0.989294,TP,ER,0.958107,TP,ER,0.989274,TP,ER,0.989273,TP,ER,0.989293 ENSG00000099785,MARCHF2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000099795,NDUFB7,FN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,FN,,1.000000 -ENSG00000099797,TECR,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000 +ENSG00000099797,TECR,FP,GR,0.000000,FP,GR,-0.000000,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000 ENSG00000099804,CDC34,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000099810,MTAP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000099817,POLR2E,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 @@ -449,7 +449,7 @@ ENSG00000100344,PNPLA3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1 ENSG00000100346,CACNA1I,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000100348,TXN2,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000100354,TNRC6B,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000100372,SLC25A17,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000 +ENSG00000100372,SLC25A17,FP->TN,BS|SU,1.000000,TN,,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000 ENSG00000100393,EP300,FN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000100412,ACO2,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000100413,POLR3H,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 @@ -470,7 +470,7 @@ ENSG00000100626,GALNT16,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,, ENSG00000100644,HIF1A,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000100652,SLC10A1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000100678,SLC8A3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000100714,MTHFD1,TP->FN,BS,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000 +ENSG00000100714,MTHFD1,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000100814,CCNB1IP1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000100867,DHRS2,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000100889,PCK2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -528,7 +528,7 @@ ENSG00000102575,ACP5,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000102699,PARP4,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000102743,SLC25A15,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000102780,DGKH,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000102794,ACOD1,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. +ENSG00000102794,ACOD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000102858,MGRN1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000102893,PHKB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000102900,NUP93,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 @@ -585,7 +585,7 @@ ENSG00000104812,GYS1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.0 ENSG00000104823,ECH1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000104879,CKM,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. ENSG00000104885,DOT1L,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 -ENSG00000104888,SLC17A7,TN,.,.,FN,.,.,TN,,0.999890,TN,.,.,TN,.,. +ENSG00000104888,SLC17A7,TN,.,.,FN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000104907,TRMT1,FN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000104951,IL4I1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000105143,SLC1A6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -722,13 +722,13 @@ ENSG00000110871,COQ5,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 ENSG00000110887,DAO,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000110911,SLC11A2,FP,BS|GR,0.000000,TN,,1.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,TN,,1.000000 ENSG00000110921,MVK,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,FP,BS|GR,0.000000 -ENSG00000110955,ATP5F1B,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,TP,ER,0.986210 +ENSG00000110955,ATP5F1B,TP,ER,0.989294,TP,ER,0.958107,TP,ER,0.989274,TP,ER,0.989273,TP,ER,0.989293 ENSG00000110958,PTGES3,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000111012,CYP27B1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000111058,ACSS3,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000 ENSG00000111077,TNS2,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000111144,LTA4H,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000111181,SLC6A12,TN,.,.,FN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000 +ENSG00000111181,SLC6A12,TN,.,.,FN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000111224,PARP11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000111261,MANSC1,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000111275,ALDH2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -737,10 +737,10 @@ ENSG00000111339,ART4,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000111371,SLC38A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000111445,RFC5,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000111581,NUP107,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 -ENSG00000111640,GAPDH,.,,0.501911,.,,0.557690,FN,,0.557678,FN,,1.000000,.,,0.500000 +ENSG00000111640,GAPDH,.,,0.501911,.,,0.557678,FN,,0.557678,FN,,1.000000,.,,0.500000 ENSG00000111666,CHPT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000111667,USP5,FN,.,.,FN,.,.,FN,.,.,FN,.,.,FN,.,. -ENSG00000111669,TPI1,TN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,0.670223 +ENSG00000111669,TPI1,TN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,0.670196 ENSG00000111670,GNPTAB,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000111674,ENO2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000111684,LPCAT3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -871,11 +871,11 @@ ENSG00000116199,FAM20B,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000116237,ICMT,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000116337,AMPD2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000116353,MECR,FN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,0.999990,FN,,1.000000 -ENSG00000116459,ATP5PB,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,FP,ER,0.986210 +ENSG00000116459,ATP5PB,TP,ER,0.989294,TP,ER,0.958107,TP,ER,0.989274,TP,ER,0.989273,FP,ER,0.989293 ENSG00000116514,RNF19B,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000116539,ASH1L,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000116649,SRM,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000116704,SLC35D1,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,TN,,1.000000 +ENSG00000116704,SLC35D1,TN,,1.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,TN,,1.000000 ENSG00000116711,PLA2G4A,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000116745,RPE65,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000116748,AMPD1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -889,7 +889,7 @@ ENSG00000117009,KMO,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000117054,ACADM,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP->TN,BS,1.000000 ENSG00000117069,ST6GALNAC5,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000117115,PADI2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000117118,SDHB,TP,ER,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 +ENSG00000117118,SDHB,TP,BS|ER|SU,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 ENSG00000117143,UAP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000117215,PLA2G2D,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000117305,HMGCL,TN,,1.000000,TN,,1.000000,TN,,0.999990,TN,,0.999990,TN,,1.000000 @@ -937,7 +937,7 @@ ENSG00000119523,ALG2,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.0 ENSG00000119537,KDSR,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000119640,ACYP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000119673,ACOT2,TN,,1.000000,FN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 -ENSG00000119689,DLST,TP,ER,1.000000,FP,ER,0.998838,TP,ER,0.998823,TP,ER,1.000000,FP,BS|ER|IC|SU,0.998838 +ENSG00000119689,DLST,TP,ER,1.000000,FP,ER,0.998838,TP,ER,0.998823,TP,ER,0.998815,FP,BS|ER|IC|SU,1.000000 ENSG00000119711,ALDH6A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP,GR,0.000000,TN,,1.000000 ENSG00000119723,COQ6,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000119772,DNMT3A,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FN,.,. @@ -954,7 +954,7 @@ ENSG00000120265,PCMT1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000120329,SLC25A2,TN,,1.000000,TN,,1.000000,FP,GR,0.000000,FP,GR,0.000000,TN,,1.000000 ENSG00000120437,ACAT2,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP->TN,BS,0.994583,FP->TN,BS,0.994583,FP,BS|GR,0.000000 ENSG00000120563,LYZL1,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. -ENSG00000120697,ALG5,TN,,0.999992,TN,,0.999992,TN,,1.000000,TN,,0.999991,TN,,0.999990 +ENSG00000120697,ALG5,TN,,0.999992,TN,,0.999992,TN,,1.000000,TN,,0.999991,TN,,0.999991 ENSG00000120820,GLT8D2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000120915,EPHX2,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000120942,UBIAD1,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. @@ -999,7 +999,7 @@ ENSG00000123453,SARDH,FP->TN,BS,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000123454,DBH,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000123505,AMD1,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000123552,USP45,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000123643,SLC36A1,TN,,1.000000,FP->TN,BS,1.000000,TN,,1.000000,FP->TN,BS,1.000000,FP->TN,BS,1.000000 +ENSG00000123643,SLC36A1,TN,,1.000000,FP->TN,BS,1.000000,TN,,1.000000,FP,BS|GR,0.000000,FP->TN,BS,1.000000 ENSG00000123684,LPGAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000123739,PLA2G12A,.,,1.000000,.,,1.000000,TN,,1.000000,TN,,1.000000,.,,1.000000 ENSG00000123836,PFKFB2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1012,7 +1012,7 @@ ENSG00000124140,SLC12A5,TN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000124151,NCOA3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000124155,PIGT,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000124164,VAPB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000124172,ATP5F1E,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 +ENSG00000124172,ATP5F1E,P,ER,0.989294,P,ER,0.958107,P,ER,0.989274,P,ER,0.989273,P,ER,0.989293 ENSG00000124181,PLCG1,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000124212,PTGIS,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000124253,PCK1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1060,8 +1060,8 @@ ENSG00000126522,ASL,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.00 ENSG00000126821,SGPP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000126883,NUP214,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 ENSG00000127080,IPPK,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000127125,PPCS,FP,BS|GR,-0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 -ENSG00000127184,COX7C,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000 +ENSG00000127125,PPCS,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,-0.000000 +ENSG00000127184,COX7C,P,BS|ER|GR|IC|SU,-0.000000,P,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000 ENSG00000127412,TRPV5,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000127415,IDUA,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000127445,PIN1,TN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1197,7 +1197,7 @@ ENSG00000133027,PEMT,FP->TN,BS,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,T ENSG00000133056,PIK3C2B,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000133063,CHIT1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000133065,SLC41A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000133116,KL,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FP,GR,0.000000 +ENSG00000133116,KL,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000133121,STARD13,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000133135,RNF128,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000133247,KMT5C,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1252,9 +1252,9 @@ ENSG00000135220,UGT2A3,.,,1.000000,.,.,.,TN,,1.000000,TN,,1.000000,.,.,. ENSG00000135226,UGT2B28,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000135241,PNPLA8,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000135318,NT5E,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000135390,ATP5MC2,FP,ER,0.989294,FP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,FP,ER,0.986210 +ENSG00000135390,ATP5MC2,FP,ER,0.989294,FP,ER,0.958107,TP,ER,0.989274,TP,ER,0.989273,FP,ER,0.989293 ENSG00000135423,GLS2,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,.,. -ENSG00000135437,RDH5,TN,,1.000000,FN,,1.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 +ENSG00000135437,RDH5,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 ENSG00000135454,B4GALNT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000135587,SMPD2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000135655,USP15,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1270,7 +1270,7 @@ ENSG00000135845,PIGC,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.0 ENSG00000135913,USP37,TN,.,.,FN,.,.,FN,.,.,TN,.,.,FN,.,. ENSG00000135917,SLC19A3,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000135929,CYP27A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000135940,COX5B,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,-0.000000 +ENSG00000135940,COX5B,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000 ENSG00000136003,ISCU,FN,.,.,FN,.,.,FN,.,.,FN,.,.,FN,.,. ENSG00000136010,ALDH1L2,TN,.,.,FP->TN,BS,1.000000,FP->TN,BS,1.000000,TN,,1.000000,TN,.,. ENSG00000136014,USP44,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1299,7 +1299,7 @@ ENSG00000136840,ST6GALNAC4,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,T ENSG00000136856,SLC2A8,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000136868,SLC31A1,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. ENSG00000136872,ALDOB,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000136877,FPGS,FN,,1.000000,FP->TN,BS,1.000000,TN,,1.000000,TP->FN,BS,1.000000,FP->TN,BS,1.000000 +ENSG00000136877,FPGS,FN,,1.000000,FP->TN,BS,1.000000,TN,,1.000000,TP,BS|GR,0.000000,FP->TN,BS,1.000000 ENSG00000136878,USP20,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000136881,BAAT,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000136888,ATP6V1G1,FN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,FN,,1.000000 @@ -1317,7 +1317,7 @@ ENSG00000137364,TPMT,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000137392,CLPS,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000137393,RNF144B,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000137491,SLCO2B1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000137563,GGH,TN,,1.000000,TP->FN,BS,1.000000,TN,,1.000000,FP->TN,BS,1.000000,FP->TN,BS,1.000000 +ENSG00000137563,GGH,TN,,1.000000,TP->FN,BS,1.000000,TN,,1.000000,FP,BS|GR,0.000000,FP->TN,BS,1.000000 ENSG00000137700,SLC37A4,P,GR,0.000000,P,GR,0.000000,P,GR,0.000000,P,GR,0.000000,P,GR,0.000000 ENSG00000137714,FDX1,TN,.,.,TN,.,.,.,.,.,TN,.,.,TN,.,. ENSG00000137731,FXYD2,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. @@ -1332,14 +1332,14 @@ ENSG00000137868,STRA6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000137869,CYP19A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000137944,KYAT3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000137968,SLC44A5,TN,,1.000000,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. -ENSG00000137992,DBT,TN,,0.999953,TN,,0.999669,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999669 +ENSG00000137992,DBT,TN,,0.999953,TN,,0.999710,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999710 ENSG00000137996,RTCA,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000138018,SELENOI,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000138029,HADHB,FP,GR|SU,0.000000,FP,GR|SU,0.000000,FP,GR|SU,0.000000,FP,GR|SU,0.000000,FP,GR|SU,0.000000 ENSG00000138030,KHK,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000138031,ADCY3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000138061,CYP1B1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP,GR,0.000000 -ENSG00000138074,SLC5A6,FP,BS|GR,-0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 +ENSG00000138074,SLC5A6,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 ENSG00000138075,ABCG5,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FN,.,. ENSG00000138079,SLC3A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000138109,CYP2C9,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 @@ -1389,7 +1389,7 @@ ENSG00000139287,TPH2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000139304,PTPRQ,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000139344,AMDHD1,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000139370,SLC15A4,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000139410,SDSL,TN,,1.000000,TN,,0.999976,TN,,0.999718,TN,,1.000000,TN,,1.000000 +ENSG00000139410,SDSL,TN,,1.000000,TN,,0.999976,TN,,0.999753,TN,,0.999981,TN,,1.000000 ENSG00000139428,MMAB,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000139433,GLTP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000139496,NUP58,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000,TP,GR,0.000000 @@ -1481,7 +1481,7 @@ ENSG00000143198,MGST3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000143199,ADCY10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000143207,COP1,TN,.,.,FN,.,.,FN,.,.,FN,.,.,TN,.,. ENSG00000143224,PPOX,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000,FP,BS|GR,0.000000 -ENSG00000143252,SDHC,P,ER,1.000000,P,ER,1.000000,FP,ER,1.000000,FP,BS|ER|SU,1.000000,P,BS|ER|SU,1.000000 +ENSG00000143252,SDHC,P,BS|ER|SU,1.000000,P,ER,1.000000,FP,ER,1.000000,FP,BS|ER|SU,1.000000,P,BS|ER|SU,1.000000 ENSG00000143258,USP21,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000143278,F13B,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000143315,PIGM,FN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 @@ -1557,7 +1557,7 @@ ENSG00000146039,SLC17A4,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000146070,PLA2G7,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000146085,MMUT,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000146151,HMGCLL1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000146233,CYP39A1,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. +ENSG00000146233,CYP39A1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000146373,RNF217,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000146411,SLC2A12,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000146414,SHPRH,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1611,7 +1611,7 @@ ENSG00000148834,GSTO1,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1. ENSG00000149016,TUT1,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000149084,HSD17B12,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000 ENSG00000149089,APIP,.,,1.000000,.,,1.000000,TN,,1.000000,TN,,1.000000,.,,1.000000 -ENSG00000149091,DGKZ,TN,,0.996655,TN,,1.000000,TN,,0.996655,TN,,0.996655,TN,,1.000000 +ENSG00000149091,DGKZ,TN,,0.996655,TN,,1.000000,TN,,0.996655,TN,,0.996615,TN,,1.000000 ENSG00000149124,GLYAT,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000149150,SLC43A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000149313,AASDHPPT,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 @@ -1660,7 +1660,7 @@ ENSG00000151729,SLC25A4,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,, ENSG00000151790,TDO2,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000 ENSG00000151883,PARP8,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000152127,MGAT5,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000152234,ATP5F1A,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,TP,ER,0.986210 +ENSG00000152234,ATP5F1A,TP,ER,0.989294,TP,ER,0.958107,TP,ER,0.989274,TP,ER,0.989273,TP,ER,0.989293 ENSG00000152254,G6PC2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000152256,PDK1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000152270,PDE3B,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,. @@ -1684,7 +1684,7 @@ ENSG00000153207,AHCTF1,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.0000 ENSG00000153253,SCN3A,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000 ENSG00000153291,SLC25A27,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000153395,LPCAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000153574,RPIA,FN,,1.000000,FP->TN,BS|IC,1.000000,TP->FN,BS|IC,1.000000,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000 +ENSG00000153574,RPIA,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000,TP,BS|GR|IC,0.000000,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000 ENSG00000153786,ZDHHC7,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000153827,TRIP12,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000153904,DDAH1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -1699,9 +1699,9 @@ ENSG00000154252,GAL3ST2,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000154269,ENPP3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000154370,TRIM11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000154447,SH3RF1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000154518,ATP5MC3,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 +ENSG00000154518,ATP5MC3,FP,ER,0.989294,FP,ER,0.958107,FP,ER,0.989274,FP,ER,0.989273,FP,ER,0.989293 ENSG00000154678,PDE1C,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000 -ENSG00000154723,ATP5PF,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 +ENSG00000154723,ATP5PF,P,ER,0.989294,P,ER,0.958107,P,ER,0.989274,P,ER,0.989273,P,ER,0.989293 ENSG00000154914,USP43,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000154930,ACSS1,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000155016,CYP2U1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1729,7 +1729,7 @@ ENSG00000156136,DCK,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.00 ENSG00000156219,ART3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000156222,SLC28A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000156256,USP16,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000156411,ATP5MJ,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 +ENSG00000156411,ATP5MJ,FP,ER,0.989294,FP,ER,0.958107,FP,ER,0.989274,FP,ER,0.989273,FP,ER,0.989293 ENSG00000156413,FUT6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000156463,SH3RF2,TN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000156467,UQCRB,FP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|SU,0.000000,FP,BS|ER|GR|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000 @@ -1787,7 +1787,7 @@ ENSG00000158865,SLC5A11,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000159063,ALG8,TN,,1.000000,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000159082,SYNJ1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000159131,GART,TP->FN,BS,1.000000,FP->TN,BS,1.000000,TP->FN,BS,1.000000,TP->FN,BS,1.000000,FP->TN,BS,1.000000 -ENSG00000159199,ATP5MC1,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 +ENSG00000159199,ATP5MC1,FP,ER,0.989294,FP,ER,0.958107,FP,ER,0.989274,FP,ER,0.989273,FP,ER,0.989293 ENSG00000159202,UBE2Z,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. ENSG00000159228,CBR1,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000159231,CBR3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1840,7 +1840,7 @@ ENSG00000160991,ORAI2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000161013,MGAT4B,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000161031,PGLYRP2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000161133,USP41P,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. -ENSG00000161217,PCYT1A,TP->FN,BS,0.982261,TN,,1.000000,TP->FN,BS,0.982262,TP->FN,BS,0.982262,FP->TN,BS,0.982261 +ENSG00000161217,PCYT1A,TP->FN,BS,0.982261,TN,,1.000000,TP->FN,BS,0.982262,TP->FN,BS,0.982264,FP->TN,BS,0.982259 ENSG00000161267,BDH1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000161281,COX7A1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000161513,FDXR,TN,.,.,TN,.,.,FN,.,.,FN,.,.,TN,.,. @@ -1898,7 +1898,7 @@ ENSG00000163406,SLC15A2,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000163481,RNF25,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000163521,GLB1L,TN,,1.000000,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000163527,STT3B,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 -ENSG00000163541,SUCLG1,FP,ER,0.998843,TP,ER,0.998843,TP,ER,0.998827,FP,ER,0.998822,FP,ER,0.998843 +ENSG00000163541,SUCLG1,FP,ER,0.998843,TP,ER,0.998843,TP,ER,0.998827,FP,ER,0.998819,FP,ER,0.998843 ENSG00000163581,SLC2A2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000163586,FABP1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000163590,PPM1L,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -1990,7 +1990,7 @@ ENSG00000165475,CRYL1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1. ENSG00000165526,RPUSD4,FN,.,.,FN,.,.,FN,.,.,FN,.,.,FN,.,. ENSG00000165591,FAAH2,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000165609,NUDT5,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000165629,ATP5F1C,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,FP,ER,0.986210 +ENSG00000165629,ATP5F1C,TP,ER,0.989294,TP,ER,0.958107,TP,ER,0.989274,TP,ER,0.989273,FP,ER,0.989293 ENSG00000165646,SLC18A2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000165671,NSD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000165672,PRDX3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2013,7 +2013,7 @@ ENSG00000166136,NDUFB8,FN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,FN,,1 ENSG00000166165,CKB,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000166169,POLL,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000166183,ASPG,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000166224,SGPL1,FP->TN,BS,0.938823,TP->FN,BS,0.938793,FP->TN,BS,0.938826,FP->TN,BS,0.938827,FP->TN,BS,0.938784 +ENSG00000166224,SGPL1,FP->TN,BS,0.938823,TP->FN,BS,0.938824,FP->TN,BS,0.938826,FP->TN,BS,0.938795,FP->TN,BS,0.938816 ENSG00000166228,PCBD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000166311,SMPD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000166340,TPP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2050,7 +2050,7 @@ ENSG00000167165,UGT1A6,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.0000 ENSG00000167186,COQ7,FP,GR,0.000000,FP,GR,0.000000,TP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 ENSG00000167261,DPEP2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000167280,ENGASE,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000167283,ATP5MG,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 +ENSG00000167283,ATP5MG,FP,ER,0.989294,FP,ER,0.958107,FP,ER,0.989274,FP,ER,0.989273,FP,ER,0.989293 ENSG00000167311,ART5,TN,.,.,TN,.,.,TN,,1.000000,TN,.,.,TN,.,. ENSG00000167315,ACAA2,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000 ENSG00000167325,RRM1,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000,TP,BS|GR,0.000000 @@ -2080,7 +2080,7 @@ ENSG00000167780,SOAT2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000167792,NDUFV1,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000167815,PRDX2,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000167862,MRPL58,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. -ENSG00000167863,ATP5PD,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 +ENSG00000167863,ATP5PD,FP,ER,0.989294,FP,ER,0.958107,FP,ER,0.989274,FP,ER,0.989273,FP,ER,0.989293 ENSG00000167889,MGAT5B,TN,.,.,FN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000167900,TK1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000167910,CYP7A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2118,14 +2118,14 @@ ENSG00000168906,MAT2A,TP,BS|GR,0.000000,FP,GR,0.000000,FN,,1.000000,TP,GR,0.0000 ENSG00000168907,PLA2G4F,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000168918,INPP5D,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,.,TN,.,. ENSG00000168938,PPIC,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000169020,ATP5ME,TP,ER,0.989294,TP,ER,0.958110,TP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 +ENSG00000169020,ATP5ME,TP,ER,0.989294,TP,ER,0.958107,TP,ER,0.989274,FP,ER,0.989273,FP,ER,0.989293 ENSG00000169021,UQCRFS1,TP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|SU,0.000000,TP,BS|ER|GR|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000 ENSG00000169100,SLC25A6,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000169105,CHST14,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000169154,GOT1L1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000169169,CPT1C,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000169180,XPO6,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 -ENSG00000169239,CA5B,TN,,1.000000,FP->TN,BS|IC,1.000000,TN,,0.999990,FP->TN,BS|IC,0.999990,FP->TN,BS|IC,1.000000 +ENSG00000169239,CA5B,FP->TN,BS|IC,1.000000,FP->TN,BS|IC,1.000000,TN,,0.999990,FP->TN,BS|IC,0.999990,TN,,1.000000 ENSG00000169255,B3GALNT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000169299,PGM2,TN,,0.665754,TN,,0.665774,TN,,0.665754,TN,,0.665754,TN,,0.998332 ENSG00000169359,SLC33A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2222,10 +2222,10 @@ ENSG00000172340,SUCLG2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1 ENSG00000172345,STARD5,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000172352,CDY1B,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000172456,FGGY,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000172461,FUT9,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. +ENSG00000172461,FUT9,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000172482,AGXT,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000172497,ACOT12,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000172508,CARNS1,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. +ENSG00000172508,CARNS1,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000172543,CTSW,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000172572,PDE3A,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,.,. ENSG00000172613,RAD9A,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 @@ -2257,16 +2257,16 @@ ENSG00000173486,FKBP2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000173540,GMPPB,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000173597,SULT1B1,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000173598,NUDT4,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000173599,PC,TN,,1.000000,FP->TN,BS|IC,1.000000,TN,,1.000000,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000 +ENSG00000173599,PC,FP->TN,BS|IC,1.000000,FP->TN,BS|IC,1.000000,TN,,1.000000,TP->FN,BS|IC,1.000000,FP->TN,BS|IC,1.000000 ENSG00000173610,UGT2A1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000173614,NMNAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000173627,APOBEC4,TN,.,.,TN,.,.,TN,.,.,FN,.,.,TN,.,. -ENSG00000173638,SLC19A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP,ER,1.000000 +ENSG00000173638,SLC19A1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP,BS|ER,1.000000 ENSG00000173660,UQCRH,FP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|SU,0.000000,FP,BS|ER|GR|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000 ENSG00000173786,CNP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000 ENSG00000173838,MARCHF10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000173868,PHOSPHO1,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. -ENSG00000173915,ATP5MK,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 +ENSG00000173915,ATP5MK,P,ER,0.989294,P,ER,0.958107,P,ER,0.989274,P,ER,0.989273,P,ER,0.989293 ENSG00000173926,MARCHF3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000174080,CTSF,TN,,1.000000,TN,,1.000000,TN,.,.,FN,,1.000000,TN,,1.000000 ENSG00000174156,GSTA3,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. @@ -2281,7 +2281,7 @@ ENSG00000174473,GALNTL6,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000,TN,,1.000000 ENSG00000174502,SLC26A9,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000174607,UGT8,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000174640,SLCO2A1,TN,.,.,TN,,1.000000,TN,.,.,TN,,1.000000,TN,.,. -ENSG00000174669,SLC29A2,TN,,0.661326,TN,,0.991864,TN,,0.991863,FN,,0.991863,TN,,0.991863 +ENSG00000174669,SLC29A2,TN,,0.661326,TN,,0.991863,TN,,0.991863,FN,,0.991864,TN,,0.991862 ENSG00000174684,B4GAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000174876,AMY1B,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000174886,NDUFA11,FN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2352,7 +2352,7 @@ ENSG00000178127,NDUFV2,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1 ENSG00000178234,GALNT11,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000178301,AQP11,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000178445,GLDC,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP->TN,BS,1.000000,TN,,1.000000 -ENSG00000178537,SLC25A20,FP->TN,BS|SU,0.978211,FP->TN,BS|SU,0.978213,FP,BS|GR|SU,0.000000,TN,,0.978267,FP,BS|GR|SU,0.000000 +ENSG00000178537,SLC25A20,FP,BS|GR|SU,0.000000,FP->TN,BS|SU,0.978261,FP,BS|GR|SU,0.000000,TN,,0.978220,FP->TN,BS|SU,0.978257 ENSG00000178685,PARP10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000178700,DHFR2,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000178741,COX5A,FP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000,FP,BS|ER|GR|IC|SU,0.000000,TP,BS|ER|GR|IC|SU,0.000000 @@ -2377,12 +2377,12 @@ ENSG00000179913,B3GNT3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1 ENSG00000179918,SEPHS2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000179958,DCTPP1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000180011,PTGR3,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000180176,TH,TN,.,.,TN,.,.,TN,.,.,TN,.,.,FN,.,. +ENSG00000180176,TH,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,FN,.,. ENSG00000180185,FAHD1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000180210,F2,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000180233,ZNRF2,.,.,.,.,.,.,FN,.,.,TN,.,.,.,.,. ENSG00000180251,SLC9A4,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000180389,ATP5F1EP2,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 +ENSG00000180389,ATP5F1EP2,P,ER,0.989294,P,ER,0.958107,P,ER,0.989274,P,ER,0.989273,P,ER,0.989293 ENSG00000180432,CYP8B1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000180537,RNF182,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000180549,FUT7,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -2469,10 +2469,10 @@ ENSG00000184788,SATL1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000184860,SDR42E1,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000184979,USP18,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000184983,NDUFA6,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000184999,SLC22A10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,,1.000000 +ENSG00000184999,SLC22A10,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000185000,DGAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000185013,NT5C1B,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. -ENSG00000185015,CA13,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,FP,BS|GR,0.000000 +ENSG00000185015,CA13,TN,,1.000000,TN,.,.,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000185052,SLC24A3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000185100,ADSS1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,FN,.,. ENSG00000185133,INPP5J,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,. @@ -2596,7 +2596,7 @@ ENSG00000197253,TPSB2,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000197296,FITM2,FN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000197323,TRIM33,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000197355,UAP1L1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000197375,SLC22A5,TN,,0.999918,TN,,1.000000,TN,,0.999918,TN,,0.999918,TN,,1.000000 +ENSG00000197375,SLC22A5,TN,,0.999918,TN,,0.999918,TN,,0.999918,TN,,1.000000,TN,,0.999918 ENSG00000197406,DIO3,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000197408,CYP2B6,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000197416,FABP12,TN,.,.,TN,.,.,FN,.,.,TN,.,.,TN,.,. @@ -2672,7 +2672,7 @@ ENSG00000198848,CES1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000198881,ASB12,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000198886,MT-ND4,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000198888,MT-ND1,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 -ENSG00000198899,MT-ATP6,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 +ENSG00000198899,MT-ATP6,P,ER,0.989294,P,ER,0.958107,P,ER,0.989274,P,ER,0.989273,P,ER,0.989293 ENSG00000198919,DZIP3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000198931,APRT,TN,,1.000000,TN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000198938,MT-CO3,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000,P,BS|ER|GR|IC|SU,0.000000 @@ -2693,7 +2693,7 @@ ENSG00000204227,RING1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000204228,HSD17B8,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,. ENSG00000204308,RNF5,TN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000204310,AGPAT1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000204370,SDHD,TP,ER,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 +ENSG00000204370,SDHD,TP,BS|ER|SU,1.000000,FP,ER,1.000000,TP,ER,1.000000,FP,BS|ER|SU,1.000000,FP,BS|ER|SU,1.000000 ENSG00000204371,EHMT2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000204385,SLC44A4,TN,,1.000000,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000204386,NEU1,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 @@ -2720,7 +2720,7 @@ ENSG00000213160,KLHL23,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1 ENSG00000213316,LTC4S,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000213339,QTRT1,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000213366,GSTM2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 -ENSG00000213398,LCAT,TN,,1.000000,TN,,0.999959,TN,,1.000000,TN,,1.000000,TN,,0.999959 +ENSG00000213398,LCAT,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,0.999959,TN,,1.000000 ENSG00000213614,HEXA,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000213619,NDUFS3,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000213648,SULT1A4,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 @@ -2749,7 +2749,7 @@ ENSG00000225697,SLC26A6,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,, ENSG00000226784,PGAM4,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000227140,USP17L5,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000227471,AKR1B15,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. -ENSG00000228253,MT-ATP8,P,ER,0.989294,P,ER,0.958110,P,ER,0.989274,P,ER,0.989278,P,ER,0.986210 +ENSG00000228253,MT-ATP8,P,ER,0.989294,P,ER,0.958107,P,ER,0.989274,P,ER,0.989273,P,ER,0.989293 ENSG00000228716,DHFR,FN,,1.000000,TN,,1.000000,FN,,1.000000,FN,,1.000000,TN,,1.000000 ENSG00000228856,USP17L30,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. ENSG00000229579,USP17L26,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. @@ -2784,15 +2784,15 @@ ENSG00000240972,MIF,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000241119,UGT1A9,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000241360,PDXP,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 ENSG00000241404,EGFL8,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 -ENSG00000241468,ATP5MF,FP,ER,0.989294,FP,ER,0.958110,FP,ER,0.989274,FP,ER,0.989278,FP,ER,0.986210 +ENSG00000241468,ATP5MF,FP,ER,0.989294,FP,ER,0.958107,FP,ER,0.989274,FP,ER,0.989273,FP,ER,0.989293 ENSG00000241635,UGT1A1,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000241644,INMT,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000241837,ATP5PO,P,ER,0.989294,P,ER,0.958110,TP,ER,0.989274,TP,ER,0.989278,P,ER,0.986210 -ENSG00000241878,PISD,FP->TN,BS,0.997079,TN,,0.997079,FN,,0.999105,FN,,0.997079,FN,,0.997079 +ENSG00000241837,ATP5PO,P,ER,0.989294,P,ER,0.958107,TP,ER,0.989274,TP,ER,0.989273,P,ER,0.989293 +ENSG00000241878,PISD,FP->TN,BS,0.995061,TN,,0.997079,FN,,0.999105,FN,,0.995062,FN,,0.997079 ENSG00000241935,HOGA1,TN,,1.000000,TN,,1.000000,TN,,1.000000,FP,GR,0.000000,TN,,1.000000 ENSG00000241973,PI4KA,TN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000,FN,,1.000000 ENSG00000242110,AMACR,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000,FP,GR,0.000000 -ENSG00000242366,UGT1A8,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 +ENSG00000242366,UGT1A8,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,0.999999 ENSG00000242515,UGT1A10,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000 ENSG00000242612,DECR2,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000,FP->TN,BS|SU,1.000000 ENSG00000243477,NAA80,TN,.,.,FN,.,.,TN,.,.,TN,.,.,TN,.,. @@ -2809,10 +2809,10 @@ ENSG00000244474,UGT1A4,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.000000,.,,1.0000 ENSG00000244486,SCARF2,TN,.,.,TN,,1.000000,TN,,1.000000,TN,.,.,TN,,1.000000 ENSG00000247626,MARS2,FN,.,.,FN,.,.,FN,.,.,FN,.,.,TN,.,. ENSG00000247746,USP51,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. -ENSG00000248098,BCKDHA,TN,,0.999953,TN,,0.999669,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999669 +ENSG00000248098,BCKDHA,TN,,0.999953,TN,,0.999710,FP,GR,0.000000,FP,GR,0.000000,TN,,0.999710 ENSG00000248144,ADH1C,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000248933,USP17L22,.,.,.,.,.,.,.,.,.,.,.,.,.,.,. -ENSG00000249222,ATP5MGL,P,ER,0.989294,P,ER,0.958110,TP,ER,0.989274,FP,ER,0.989278,P,ER,0.986210 +ENSG00000249222,ATP5MGL,P,ER,0.989294,P,ER,0.958107,TP,ER,0.989274,FP,ER,0.989273,P,ER,0.989293 ENSG00000249853,HS3ST5,TN,.,.,TN,,1.000000,TN,.,.,TN,.,.,TN,.,. ENSG00000249948,GBA3,TN,.,.,TN,.,.,TN,.,.,TN,.,.,TN,.,. ENSG00000250565,ATP6V1E2,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000,TN,,1.000000 diff --git a/data/testResults/gene-essential_summary.md b/data/testResults/gene-essential_summary.md index b75c2dce8..670a0b08d 100644 --- a/data/testResults/gene-essential_summary.md +++ b/data/testResults/gene-essential_summary.md @@ -6,27 +6,29 @@ Scored over every model gene that Hart 2015 scored in the cell line (`genes`); a | cellLine | genes | allTaskMCC | allTaskFP | viabilityMCC | viabilityFP | growthAUROC | growthAUPRC | baseRate | capabilityOnly | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | -| DLD1 | 2652 | 0.3427 | 134 | 0.3632 | 100 | 0.644 | 0.2653 | 0.1259 | 42 | -| GBM | 2652 | 0.2905 | 141 | 0.3118 | 109 | 0.6235 | 0.2419 | 0.1316 | 38 | -| HCT116 | 2712 | 0.3585 | 126 | 0.3527 | 107 | 0.6451 | 0.2758 | 0.1394 | 31 | -| HELA | 2714 | 0.3118 | 164 | 0.3038 | 138 | 0.6433 | 0.2234 | 0.1102 | 38 | -| RPE1 | 2652 | 0.2315 | 171 | 0.2607 | 136 | 0.6183 | 0.1963 | 0.1086 | 37 | -| all | 2649 | 0.307 | 170 | 0.3269 | 144 | 0.635 | 0.2401 | 0.1232 | | +| DLD1 | 2652 | 0.3405 | 136 | 0.3619 | 101 | 0.6439 | 0.2644 | 0.1259 | 43 | +| GBM | 2652 | 0.2943 | 140 | 0.3147 | 109 | 0.6247 | 0.2437 | 0.1316 | 37 | +| HCT116 | 2712 | 0.3585 | 126 | 0.3553 | 107 | 0.6465 | 0.2776 | 0.1394 | 30 | +| HELA | 2714 | 0.3118 | 164 | 0.3049 | 140 | 0.6463 | 0.2251 | 0.1102 | 35 | +| RPE1 | 2652 | 0.2341 | 168 | 0.2638 | 133 | 0.6185 | 0.1982 | 0.1086 | 37 | +| all | 2649 | 0.3061 | 171 | 0.3258 | 145 | 0.6362 | 0.2415 | 0.1232 | | ### Run environment - cobra 0.32.1, gurobipy 13.0.3, optlang 1.9.1, python 3.11.17, raven-toolbox 3.0.0b1, raven-toolbox commit ee0f8868bcc4a6f907913151a1e54dcbb4f2a160 ftINIT steps that kept an unproven incumbent (time limit or unconverged tie-break): -- HELA (reaction order 0): 1 warning(s) - RPE1 (reaction order 0): 1 warning(s) ### Gene essentiality: effect of this change (vs `develop`) -Checked **50** gene(s) directly affected plus **1839** more that share a metabolite with one of them. +Checked **51** gene(s) directly affected plus **1828** more that share a metabolite with one of them. -**Likely noise** (5 gene(s), <3/5 lines): CA5B, KL, MTHFD1, PC, RDH5. +**Other role changed** (not Hart-comparable): +- CA5B: 3/5 lines, biosynthesis, internal conversion -- now required -**No change:** 1884 gene(s). +**Likely noise** (5 gene(s), <3/5 lines): CA13, FPGS, GGH, SLC25A17, SLC36A1. + +**No change:** 1873 gene(s). Full per-gene, per-line detail (every gene checked, not just the ones named above): [gene-essential-diff.csv](gene-essential-diff.csv).