From ccc8b29ba9b9ce9a09cb15ed09b04c996fc4c851 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer <33460176+Devlin-Moyer@users.noreply.github.com> Date: Mon, 16 Dec 2024 19:16:15 -0500 Subject: [PATCH 01/16] Fix Duplicate Stearoyl-CoA Beta-Oxidation Reactions (#820) * fix: removed MAR00776 and MAR00778 from YAML file * feat: added appropriate refs for MAR03115-8 since refs from MAR00776 weren't appropriate * chore: merged annotations for MAR00776 with those for MAR03115-8 in reactions.tsv and moved MAR00776 to deprecatedReactions.tsv * chore: merged annotations for MAR00778 with those for MAR03116-MAR03146 in reactions.tsv and moved MAR00778 to deprecatedReactions.tsv * fix: indentation error in YAML file * fix: removed incorrect MetaNetX IDs for MAR03117 and MAR03118 * chore: add macaw test result * chore: add macaw test result --------- Co-authored-by: Eduard Kerkhoven Co-authored-by: Devlin-Moyer Co-authored-by: edkerk --- .../deprecatedReactions.tsv | 2 + data/testResults/README.md | 2 +- data/testResults/macaw_results.csv | 2 - model/Human-GEM.yml | 56 ++----------------- model/reactions.tsv | 42 +++++++------- 5 files changed, 27 insertions(+), 77 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 69cfefad..39779b48 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -300,3 +300,5 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR08745" "" "THMMPtm" "" "" "" "" "MNXR104822" "HMR_8745" "RCR20669" "" 0 "" "" "HMR_8745" "MAR08747" "" "THMPPtm" "" "" "" "" "MNXR104824" "HMR_8747" "RCR20670" "" 0 "" "" "HMR_8747" "MAR07799" "" "ATPasel" "" "" "" "" "MNXR96136" "HMR_7799" "RCR20334" "" 0 "" "" "HMR_7799" +"MAR00776" "" "FAOXC180" "" "" "" "FAOXC180" "MNXR99313" "" "" "" 0 "" "" "FAOXC180" +"MAR00778" "" "FAOXC1811601m" "" "" "" "FAOXC1811601m" "MNXR99315" "" "" "" 0 "" "" "FAOXC1811601m" diff --git a/data/testResults/README.md b/data/testResults/README.md index 39140d5d..5a49a7d3 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #933** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #820** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv index aa73eeed..112e0ccf 100644 --- a/data/testResults/macaw_results.csv +++ b/data/testResults/macaw_results.csv @@ -8250,9 +8250,7 @@ MAR00759,4 MAM01597x + 4 MAM01802x + 4 MAM02040x + 4 MAM02552x + MAM02678x --> 4 MAR00764,MAM00051m + 4 MAM01597m + 3 MAM01802m + 4 MAM02040m + 4 MAM02552m --> 4 MAM01261m + 3 MAM01803m + 4 MAM02039m + 4 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00772,4 MAM01597m + 3 MAM01802m + 4 MAM02040m + 4 MAM02552m + MAM02677m --> 4 MAM01261m + 3 MAM01803m + 4 MAM02039m + 4 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00774,7 MAM01597m + 7 MAM01802m + 7 MAM02040m + MAM02101m + 7 MAM02552m --> 7 MAM01261m + 7 MAM01803m + 7 MAM02039m + 7 MAM02553m + MAM02774m,ok,ok,ok,ok,N/A -MAR00776,MAM01597m + MAM01802m + MAM02040m + MAM02552m + MAM02941m --> MAM01261m + MAM01803m + MAM02039m + MAM02553m + MAM02678m,ok,ok,ok,ok,N/A MAR00777,MAM01597x + MAM01802x + MAM02040x + MAM02552x + MAM02941x --> MAM01261x + MAM01803x + MAM02039x + MAM02553x + MAM02678x,ok,ok,ok,ok,N/A -MAR00778,MAM00057m + 5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00780,5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m + MAM03791m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00784,5 MAM01597m + 4 MAM01802m + 5 MAM02040m + 5 MAM02552m + MAM02647m --> 5 MAM01261m + 4 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A MAR00785,5 MAM01597m + 3 MAM01802m + 5 MAM02040m + MAM02391m + 5 MAM02552m --> 5 MAM01261m + 3 MAM01803m + 5 MAM02039m + 5 MAM02553m + MAM02644m,ok,ok,ok,ok,N/A diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 5f1cbb0c..568b3f1d 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -118350,7 +118350,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.3.8.7;1.3.8.8;1.3.8.9;1.3.99.-" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -118367,7 +118367,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.17" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -118386,7 +118386,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.35;1.1.1.211" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -118404,7 +118404,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.16;1.1.1.211" - - references: "" + - references: "PMID:20490924" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -221482,30 +221482,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR00776" - - name: "Beta Oxidation of Long Chain Fatty Acid" - - metabolites: !!omap - - MAM01261m: 1 - - MAM01597m: -1 - - MAM01802m: -1 - - MAM01803m: 1 - - MAM02039m: 1 - - MAM02040m: -1 - - MAM02552m: -1 - - MAM02553m: 1 - - MAM02678m: 1 - - MAM02941m: -1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "1.3.99.3" - - references: "PMID:2565344;PMID:3035565" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR00777" - name: "Beta Oxidation of Long Chain Fatty Acid" @@ -221530,30 +221506,6 @@ - subsystem: - "Fatty acid oxidation" - confidence_score: 0 - - !!omap - - id: "MAR00778" - - name: "Beta Oxidation Fatty Acid" - - metabolites: !!omap - - MAM00057m: -1 - - MAM01261m: 5 - - MAM01597m: -5 - - MAM01802m: -4 - - MAM01803m: 4 - - MAM02039m: 5 - - MAM02040m: -5 - - MAM02552m: -5 - - MAM02553m: 5 - - MAM02644m: 1 - - lower_bound: 0 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971" - - rxnNotes: "" - - rxnFrom: "Recon3D" - - eccodes: "4.2.1.74" - - references: "" - - subsystem: - - "Fatty acid oxidation" - - confidence_score: 0 - !!omap - id: "MAR00780" - name: "Beta Oxidation Fatty Acid" diff --git a/model/reactions.tsv b/model/reactions.tsv index 1a9770d5..4fa8c7c9 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -2624,26 +2624,26 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR03112" "" "" "" "" "" "HMR_3112" "" "HMR_3112" "RCR12626" "" 0 "" "" "HMR_3112" "MAR03113" "" "" "" "" "" "HMR_3113" "" "HMR_3113" "RCR12627" "" 0 "" "" "HMR_3113" "MAR03114" "" "" "" "" "" "HMR_3114" "" "HMR_3114" "RCR12628" "" 0 "" "" "HMR_3114" -"MAR03115" "" "" "" "" "" "HMR_3115" "" "HMR_3115" "RCR12629" "" 0 "" "" "HMR_3115" -"MAR03116" "R07760" "" "" "" "" "HMR_3116" "" "HMR_3116" "RCR12630" "" 0 "RHEA:35349" "RHEA:35347" "HMR_3116" -"MAR03117" "" "" "" "" "" "HMR_3117" "" "HMR_3117" "RCR12631" "" 0 "RHEA:35276" "RHEA:35275" "HMR_3117" -"MAR03118" "" "" "" "" "" "HMR_3118" "" "HMR_3118" "RCR12632" "" 0 "" "" "HMR_3118" -"MAR03121" "R01279" "r0310" "" "" "R-HSA-77299" "HMR_3121;r0310" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310;MAR02035" -"MAR03122" "R04738" "" "R04738X" "r0716" "" "r0716" "MNXR105372;MNXR97892" "HMR_3122" "RCR12634" "" 0 "" "RHEA:31163" "HMR_3122" -"MAR03123" "R04737" "" "R04737X" "r0714" "" "r0714" "MNXR100548;MNXR105371" "HMR_3123" "RCR12635" "" 0 "" "RHEA:31159" "HMR_3123" -"MAR03125" "R03991" "" "R03991X" "r0653" "" "r0653" "MNXR95203" "HMR_3125" "RCR12636" "" 0 "" "RHEA:18161" "HMR_3125" -"MAR03128" "R03990" "r1449" "" "" "R-HSA-77274" "HMR_3128;r1449" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449;MAR02370" -"MAR03129" "R04740" "" "R04740X" "r0720" "" "r0720" "MNXR105373;MNXR97891" "HMR_3129" "RCR12638" "" 0 "" "RHEA:31171" "HMR_3129" -"MAR03130" "R04739" "" "R04739X" "r0718" "" "r0718" "MNXR100547" "HMR_3130" "RCR12639" "" 0 "" "RHEA:31167" "HMR_3130" -"MAR03132" "R03858" "" "R03858X" "r0639" "" "r0639" "MNXR95201" "HMR_3132" "RCR12640" "" 0 "" "RHEA:31091" "HMR_3132" -"MAR03135" "R03857" "r1447" "" "" "R-HSA-77263" "HMR_3135;r1447" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447;MAR02367" -"MAR03136" "R04170" "r1446" "R04170X" "r0660" "" "r0660;r1446" "MNXR97890" "HMR_3136" "RCR12642" "" 0 "" "RHEA:31075" "HMR_3136;r1446;MAR02366" -"MAR03137" "R04741" "" "R04741X" "r0722" "" "r0722" "MNXR100546" "HMR_3137" "RCR12643" "" 0 "" "RHEA:31179" "HMR_3137" -"MAR03139" "R04742" "" "R04742X" "r0724" "" "r0724" "MNXR95199;MNXR95200" "HMR_3139" "RCR12644" "" 0 "RHEA:31185" "RHEA:31183" "HMR_3139" -"MAR03142" "R04754" "r1451;FAOXC10C10OHm;FAOXC10080m" "" "" "R-HSA-77345" "HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024" -"MAR03143" "R04744" "FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m" "R04744X" "r0728" "" "r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m" "MNXR97889" "HMR_3143;HMR_3422" "RCR12646;RCR12667" "" 0 "" "RHEA:31191" "HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024" -"MAR03144" "R04743" "FAOXC101C8m;FAOXC10080m" "R04743X" "r0726" "" "r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m" "MNXR100545" "HMR_3144;HMR_3422" "RCR12647;RCR12667" "" 0 "" "RHEA:31187" "HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024" -"MAR03146" "R03778" "FAOXC101C8m;FAOXC10080m" "R03778X" "r0634" "" "r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m" "MNXR95198" "HMR_3146;HMR_3422" "RCR12648;RCR12667" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024" +"MAR03115" "" "FAOXC180" "" "" "" "HMR_3115;FAOXC180" "" "HMR_3115" "RCR12629" "" 0 "" "" "HMR_3115;FAOXC180;MAR00776" +"MAR03116" "R07760" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3116;FAOXC180;FAOXC1811601m" "" "HMR_3116" "RCR12630" "" 0 "RHEA:35349" "RHEA:35347" "HMR_3116;FAOXC180;MAR00776;FAOXC1811601m;MAR00778" +"MAR03117" "" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3117;FAOXC180;FAOXC1811601m" "" "HMR_3117" "RCR12631" "" 0 "RHEA:35276" "RHEA:35275" "HMR_3117;FAOXC180;MAR00776;FAOXC1811601m;MAR00778" +"MAR03118" "" "FAOXC180;FAOXC1811601m" "" "" "" "HMR_3118;FAOXC180;FAOXC1811601m" "" "HMR_3118" "RCR12632" "" 0 "" "" "HMR_3118;FAOXC180;MAR00776;FAOXC1811601m;MAR00778" +"MAR03121" "R01279" "r0310;FAOXC1811601m" "" "" "R-HSA-77299" "HMR_3121;r0310;FAOXC1811601m" "MNXR125070" "HMR_3121" "RCR12633" "" 0 "" "RHEA:30747" "HMR_3121;r0310;MAR02035;FAOXC1811601m;MAR00778" +"MAR03122" "R04738" "FAOXC1811601m" "R04738X" "r0716" "" "r0716;FAOXC1811601m" "MNXR105372;MNXR97892" "HMR_3122" "RCR12634" "" 0 "" "RHEA:31163" "HMR_3122;FAOXC1811601m;MAR00778" +"MAR03123" "R04737" "FAOXC1811601m" "R04737X" "r0714" "" "r0714;FAOXC1811601m" "MNXR100548;MNXR105371" "HMR_3123" "RCR12635" "" 0 "" "RHEA:31159" "HMR_3123;FAOXC1811601m;MAR00778" +"MAR03125" "R03991" "FAOXC1811601m" "R03991X" "r0653" "" "r0653;FAOXC1811601m" "MNXR95203" "HMR_3125" "RCR12636" "" 0 "" "RHEA:18161" "HMR_3125;FAOXC1811601m;MAR00778" +"MAR03128" "R03990" "r1449;FAOXC1811601m" "" "" "R-HSA-77274" "HMR_3128;r1449;FAOXC1811601m" "MNXR95300" "HMR_3128" "RCR12637" "" 0 "" "RHEA:28358" "HMR_3128;r1449;MAR02370;FAOXC1811601m;MAR00778" +"MAR03129" "R04740" "FAOXC1811601m" "R04740X" "r0720" "" "r0720;FAOXC1811601m" "MNXR105373;MNXR97891" "HMR_3129" "RCR12638" "" 0 "" "RHEA:31171" "HMR_3129;FAOXC1811601m;MAR00778" +"MAR03130" "R04739" "FAOXC1811601m" "R04739X" "r0718" "" "r0718;FAOXC1811601m" "MNXR100547" "HMR_3130" "RCR12639" "" 0 "" "RHEA:31167" "HMR_3130;FAOXC1811601m;MAR00778" +"MAR03132" "R03858" "FAOXC1811601m" "R03858X" "r0639" "" "r0639;FAOXC1811601m" "MNXR95201" "HMR_3132" "RCR12640" "" 0 "" "RHEA:31091" "HMR_3132;FAOXC1811601m;MAR00778" +"MAR03135" "R03857" "r1447;FAOXC1811601m" "" "" "R-HSA-77263" "HMR_3135;r1447;FAOXC1811601m" "MNXR95299" "HMR_3135" "RCR12641" "" 0 "" "RHEA:31039" "HMR_3135;r1447;MAR02367;FAOXC1811601m;MAR00778" +"MAR03136" "R04170" "r1446;FAOXC1811601m" "R04170X" "r0660" "" "r0660;r1446;FAOXC1811601m" "MNXR97890" "HMR_3136" "RCR12642" "" 0 "" "RHEA:31075" "HMR_3136;r1446;MAR02366;FAOXC1811601m;MAR00778" +"MAR03137" "R04741" "FAOXC1811601m" "R04741X" "r0722" "" "r0722;FAOXC1811601m" "MNXR100546" "HMR_3137" "RCR12643" "" 0 "" "RHEA:31179" "HMR_3137;FAOXC1811601m;MAR00778" +"MAR03139" "R04742" "FAOXC1811601m" "R04742X" "r0724" "" "r0724;FAOXC1811601m" "MNXR95199;MNXR95200" "HMR_3139" "RCR12644" "" 0 "RHEA:31185" "RHEA:31183" "HMR_3139;FAOXC1811601m;MAR00778" +"MAR03142" "R04754" "r1451;FAOXC10C10OHm;FAOXC10080m;FAOXC1811601m" "" "" "R-HSA-77345" "HMR_3142;r1451;FAOXC10C10OHm;FAOXC10C8m;FAOXC1811601m" "MNXR109095" "HMR_3142" "RCR12645" "" 0 "" "RHEA:28354" "HMR_3142;r1451;MAR02373;FAOXC10C10OHm;MAR05019;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" +"MAR03143" "R04744" "FAOXC10C10OHm;FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R04744X" "r0728" "" "r0728;HMR_3422;FAOXC10C10OHm;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR97889" "HMR_3143;HMR_3422" "RCR12646;RCR12667" "" 0 "" "RHEA:31191" "HMR_3143;HMR_3422;MAR03422;FAOXC10C10OHm;MAR05019;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" +"MAR03144" "R04743" "FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R04743X" "r0726" "" "r0726;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR100545" "HMR_3144;HMR_3422" "RCR12647;RCR12667" "" 0 "" "RHEA:31187" "HMR_3144;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" +"MAR03146" "R03778" "FAOXC101C8m;FAOXC10080m;FAOXC1811601m" "R03778X" "r0634" "" "r0634;HMR_3422;FAOXC101C8m;FAOXC10C8m;FAOXC1811601m" "MNXR95198" "HMR_3146;HMR_3422" "RCR12648;RCR12667" "" 0 "RHEA:31089" "RHEA:31087" "HMR_3146;HMR_3422;MAR03422;FAOXC101C8m;MAR04967;FAOXC10C8m;MAR05024;FAOXC1811601m;MAR00778" "MAR03149" "R03777" "r1448;FAOXC8C6m;FAOXC80" "" "" "R-HSA-77338" "HMR_3149;r1448;FAOXC6C8m;FAOXC80;HMR_3422" "MNXR95304" "HMR_3149;HMR_3422" "RCR12649;RCR12667" "" 0 "" "RHEA:30943" "HMR_3149;r1448;MAR02369;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422" "MAR03150" "R04746" "FAOXC8C6m;FAOXC80" "R04746M" "r0731" "" "r0731;FAOXC8C6m;FAOXC80;HMR_3422" "MNXR97888" "HMR_3150;HMR_3422" "RCR12650;RCR12667" "" 0 "" "RHEA:31199" "HMR_3150;FAOXC6C8m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422" "MAR03151" "R04745" "FAOXC8C6m;FAOXC80" "R04745M" "r0730" "" "r0730;FAOXC8C6m;FAOXC80;HMR_3422" "MNXR100544" "HMR_3151;HMR_3422" "RCR12651;RCR12667" "" 0 "" "RHEA:31195" "HMR_3151;FAOXC8C6m;MAR06329;FAOXC80;MAR01009;HMR_3422;MAR03422" @@ -8249,9 +8249,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR00764" "" "FAOXC161802m" "" "" "" "FAOXC161802m" "MNXR99301" "" "" "" 0 "" "" "FAOXC161802m" "MAR00772" "" "FAOXC16180m" "" "" "" "FAOXC16180m" "MNXR99302" "" "" "" 0 "" "" "FAOXC16180m" "MAR00774" "" "FAOXC170m" "" "" "" "FAOXC170m" "MNXR99312" "" "" "" 0 "" "" "FAOXC170m" -"MAR00776" "" "FAOXC180" "" "" "" "FAOXC180" "MNXR99313" "" "" "" 0 "" "" "FAOXC180" "MAR00777" "" "FAOXC180x" "" "" "" "FAOXC180x" "MNXR99314" "" "" "" 0 "" "" "FAOXC180x" -"MAR00778" "" "FAOXC1811601m" "" "" "" "FAOXC1811601m" "MNXR99315" "" "" "" 0 "" "" "FAOXC1811601m" "MAR00780" "" "FAOXC1811602m" "" "" "" "FAOXC1811602m" "MNXR99316" "" "" "" 0 "" "" "FAOXC1811602m" "MAR00784" "" "FAOXC1811603m" "" "" "" "FAOXC1811603m" "MNXR99317" "" "" "" 0 "" "" "FAOXC1811603m" "MAR00785" "" "FAOXC182806m" "" "" "" "FAOXC182806m" "MNXR99321" "" "" "" 0 "" "" "FAOXC182806m" From ba8a4f3c02e929dda9bd2daa964cc3433318cd65 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:39:41 +0800 Subject: [PATCH 02/16] Fix-GPR curation for fatty_acid_oxidation and Glycerolipid_metabolism (#928) * fix: GPR curation for fatty_acid_oxidation and Glycerolipid_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- data/testResults/README.md | 2 +- model/Human-GEM.yml | 24 ++++++++++++------------ 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 5a49a7d3..78746c32 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #820** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #928** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 568b3f1d..ca0b3fe0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -131779,7 +131779,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1;1.1.1.2;1.1.1.21;1.1.1.72" @@ -131818,7 +131818,7 @@ - MAM02555m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1;1.1.1.2;1.1.1.21;1.1.1.72" @@ -134237,7 +134237,7 @@ - MAM02877c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135929" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.1.1.103" @@ -134255,7 +134255,7 @@ - MAM02877c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135929" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.1.1.103" @@ -223471,7 +223471,7 @@ - MAM03727c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "2.3.1.21" @@ -231805,7 +231805,7 @@ - MAM03333m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000161533 or ENSG00000196177" + - gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000196177" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.3.99.3" @@ -232279,7 +232279,7 @@ - MAM02766x: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000068366 or ENSG00000103740 or ENSG00000119673 or ENSG00000123983 or ENSG00000130377 or ENSG00000140284 or ENSG00000151726 or ENSG00000164398 or ENSG00000177465 or ENSG00000197142" + - gene_reaction_rule: "ENSG00000140284" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "6.2.1.3" @@ -237338,7 +237338,7 @@ - MAM03488c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -237917,7 +237917,7 @@ - MAM03496c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -241061,7 +241061,7 @@ - MAM03243c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "http://www.perkinelmergenetics.com/3Hydroxy3MethylglutarylCoALyaseDeficiency.html" - rxnFrom: "Recon3D" - eccodes: "" @@ -241163,7 +241163,7 @@ - MAM03409x: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000060971 and ENSG00000113790 and ENSG00000133835 and ENSG00000161533" + - gene_reaction_rule: "(ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835) and (ENSG00000060971 or ENSG00000116171)" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -272528,7 +272528,7 @@ - MAM03922x: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000113790 and ENSG00000161533) or (ENSG00000104823 and ENSG00000161533)" + - gene_reaction_rule: "(ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835)" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.3.3.6;4.2.1.17" From dcfcf71f8a21cf60a1e78366954c48330d449c43 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:43:50 +0800 Subject: [PATCH 03/16] Fix gpr curation for histidine metabolism, propanoate metabolism and nucleotide metabolism (#884) * Fix-GPR curation for Histidine metabolism/Propanoate metabolism/Nucleotide metabolism * Fix-remove unused genes * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 65 +++++++++++++++++++-------------------------- model/genes.tsv | 3 --- 2 files changed, 28 insertions(+), 40 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index ca0b3fe0..00b60dbc 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -70769,7 +70769,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116133" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.59" @@ -70847,7 +70847,7 @@ - MAM03168m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857" + - gene_reaction_rule: "ENSG00000100867 or ENSG00000109854 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.-" @@ -74688,7 +74688,7 @@ - MAM02759m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125877" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.6.1.19" @@ -74724,7 +74724,7 @@ - MAM01755c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000168393" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.9" @@ -75044,7 +75044,7 @@ - MAM02039c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196839" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.76;2.7.1.76" @@ -75062,7 +75062,7 @@ - MAM01755m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000168393" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.4;2.7.4.9" @@ -75293,7 +75293,7 @@ - MAM02751l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -75311,7 +75311,7 @@ - MAM03123l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -75347,7 +75347,7 @@ - MAM02751l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -75365,7 +75365,7 @@ - MAM02996l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000116981 or ENSG00000125458 or ENSG00000135318 or ENSG00000185013 or ENSG00000205309" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.-" @@ -75383,7 +75383,7 @@ - MAM02751l: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -75795,7 +75795,7 @@ - MAM03130m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" + - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.6" @@ -75921,7 +75921,7 @@ - MAM01645m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" + - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.6" @@ -76011,7 +76011,7 @@ - MAM02193m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" + - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000155085 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.6" @@ -76029,7 +76029,7 @@ - MAM02040n: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268" + - gene_reaction_rule: "ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.4.35" @@ -76047,7 +76047,7 @@ - MAM02040g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268" + - gene_reaction_rule: "ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000172572 or ENSG00000185527 or ENSG00000186642" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.4.17" @@ -76065,7 +76065,7 @@ - MAM02040g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268" + - gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.4.17" @@ -76084,7 +76084,7 @@ - MAM02040c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165609 or ENSG00000170222 or ENSG00000170502" + - gene_reaction_rule: "ENSG00000165609 or ENSG00000170222" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.6.1.13" @@ -76103,7 +76103,7 @@ - MAM02454c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000165609 or ENSG00000170222 or ENSG00000170502" + - gene_reaction_rule: "ENSG00000165609 or ENSG00000170222" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.6.1.13" @@ -76194,7 +76194,7 @@ - MAM01688c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000162368" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.14" @@ -76623,7 +76623,7 @@ - MAM02751e: 2 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000054179 or ENSG00000138185 or ENSG00000168032 or ENSG00000171302 or ENSG00000187097 or ENSG00000188833 or ENSG00000197217 or ENSG00000197586" + - gene_reaction_rule: "ENSG00000054179 or ENSG00000138185 or ENSG00000168032 or ENSG00000187097 or ENSG00000188833 or ENSG00000197217 or ENSG00000197586" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.6.1.5;3.6.1.6;3.6.1.42" @@ -80558,7 +80558,7 @@ - MAM02039c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000102030 or ENSG00000122390 or ENSG00000139977 or ENSG00000156269 or ENSG00000164134 or ENSG00000173418" + - gene_reaction_rule: "ENSG00000102030 or ENSG00000122390 or ENSG00000164134" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.88" @@ -80576,7 +80576,7 @@ - MAM02125c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000132437 or ENSG00000140287" + - gene_reaction_rule: "ENSG00000140287" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.1.22;4.1.1.28" @@ -80727,7 +80727,7 @@ - MAM02867c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000078124 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000138744 or ENSG00000142082 or ENSG00000156795 or ENSG00000157045 or ENSG00000172264 or ENSG00000187531" + - gene_reaction_rule: "ENSG00000077463 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000142082 or ENSG00000156795 or ENSG00000157045 or ENSG00000187531" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.5.1.-" @@ -80744,7 +80744,7 @@ - MAM03124c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000054267 or ENSG00000117682 or ENSG00000120942 or ENSG00000183665" + - gene_reaction_rule: "ENSG00000054267 or ENSG00000120942" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.5.1.-" @@ -80763,7 +80763,7 @@ - MAM02867c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000012660 or ENSG00000066322 or ENSG00000118402 or ENSG00000119915 or ENSG00000164181 or ENSG00000170522 or ENSG00000197977" + - gene_reaction_rule: "ENSG00000066322 or ENSG00000119915 or ENSG00000164181 or ENSG00000197977" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.199" @@ -80781,7 +80781,7 @@ - MAM02867c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000078124 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000138744 or ENSG00000142082 or ENSG00000156795 or ENSG00000157045 or ENSG00000172264 or ENSG00000187531" + - gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000138744 or ENSG00000142082 or ENSG00000157045 or ENSG00000172264 or ENSG00000187531" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.5.1.-" @@ -80799,7 +80799,7 @@ - MAM02867c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000078124 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000133315 or ENSG00000138744 or ENSG00000142082 or ENSG00000156795 or ENSG00000157045 or ENSG00000172264 or ENSG00000187531" + - gene_reaction_rule: "ENSG00000068903 or ENSG00000077463 or ENSG00000096717 or ENSG00000124523 or ENSG00000124596 or ENSG00000132744 or ENSG00000156795 or ENSG00000157045 or ENSG00000187531" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.5.1.-" @@ -308873,9 +308873,6 @@ - !!omap - id: "ENSG00000139914" - name: "FITM1" - - !!omap - - id: "ENSG00000139977" - - name: "NAA30" - !!omap - id: "ENSG00000139988" - name: "RDH12" @@ -309869,9 +309866,6 @@ - !!omap - id: "ENSG00000156256" - name: "USP16" - - !!omap - - id: "ENSG00000156269" - - name: "NAA11" - !!omap - id: "ENSG00000156411" - name: "ATP5MJ" @@ -312020,9 +312014,6 @@ - !!omap - id: "ENSG00000183654" - name: "MARCHF11" - - !!omap - - id: "ENSG00000183665" - - name: "TRMT12" - !!omap - id: "ENSG00000183696" - name: "UPP1" diff --git a/model/genes.tsv b/model/genes.tsv index 73213a76..5ec73e81 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -1408,7 +1408,6 @@ ENSG00000139631 "ENST00000267085;ENST00000475890;ENST00000379850;ENST00000379846 ENSG00000139684 "ENST00000378720;ENST00000378697;ENST00000412582;ENST00000471867;ENST00000495654" "ENSP00000367992;ENSP00000367969;ENSP00000391350;ENSP00000476193" P10768 ESD 2098 esterase D "Golgi apparatus;Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000139718 "ENST00000604567;ENST00000542440;ENST00000619791;ENST00000267197" "ENSP00000474253;ENSP00000442924;ENSP00000481531;ENSP00000267197" Q9UPS6 SETD1B 23067 SET domain containing 1B, histone lysine methyltransferase "KIAA1076;KMT2G;Set1B" Nucleus "SwissProt;CellAtlas" ENSG00000139914 "ENST00000267426;ENST00000559294" "ENSP00000267426;ENSP00000453741" A5D6W6 FITM1 161247 fat storage inducing transmembrane protein 1 FIT1 Endoplasmic reticulum DeepLoc2 -ENSG00000139977 "ENST00000555166;ENST00000556492;ENST00000554703;ENST00000298406" "ENSP00000450939;ENSP00000452521;ENSP00000451255;ENSP00000298406" Q147X3 NAA30 122830 N-alpha-acetyltransferase 30, NatC catalytic subunit "C14orf35;FLJ35355;MAK3;Mak3p;NAT12" "Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000139988 "ENST00000551171;ENST00000547463;ENST00000267502;ENST00000552873" "ENSP00000449079;ENSP00000267502" Q96NR8 RDH12 145226 retinol dehydrogenase 12 "FLJ30273;LCA13;RP53;SDR7C2" Endoplasmic reticulum SwissProt ENSG00000140057 "ENST00000267584;ENST00000555570;ENST00000556643;ENST00000554313;ENST00000554706" "ENSP00000267584;ENSP00000451068;ENSP00000450453" Q96M32 AK7 122481 adenylate kinase 7 "CFAP75;FAP75;FLJ32864" Cytosol SwissProt ENSG00000140090 "ENST00000393265;ENST00000532405;ENST00000676001;ENST00000531433;ENST00000554461;ENST00000525557;ENST00000554925;ENST00000556739;ENST00000526482" "ENSP00000376948;ENSP00000431840;ENSP00000502715;ENSP00000433302;ENSP00000452099;ENSP00000432464" Q8NFF2 SLC24A4 123041 solute carrier family 24 member 4 NCKX4 Cytosol SwissProt @@ -1738,7 +1737,6 @@ ENSG00000156136 "ENST00000509617;ENST00000286648;ENST00000503359;ENST00000504730 ENSG00000156219 "ENST00000513353;ENST00000510669;ENST00000341029;ENST00000513122;ENST00000504914;ENST00000355810;ENST00000349321;ENST00000513494;ENST00000510423;ENST00000395688;ENST00000504112;ENST00000506667;ENST00000506313;ENST00000511188;ENST00000510863" "ENSP00000421345;ENSP00000343843;ENSP00000422287;ENSP00000421431;ENSP00000348064;ENSP00000304313;ENSP00000425327;ENSP00000422249" Q13508 ART3 419 ADP-ribosyltransferase 3 (inactive) ARTC3 Cell membrane DeepLoc2 ENSG00000156222 "ENST00000338602;ENST00000538177;ENST00000394573;ENST00000286749" "ENSP00000341629;ENSP00000443752;ENSP00000378074;ENSP00000286749" O00337 SLC28A1 9154 solute carrier family 28 member 1 CNT1 "Cytosol;Nucleus" CellAtlas ENSG00000156256 "ENST00000399975;ENST00000399976;ENST00000334352;ENST00000474835;ENST00000399973;ENST00000485067" "ENSP00000382857;ENSP00000382858;ENSP00000334808;ENSP00000382855" Q9Y5T5 USP16 10600 ubiquitin specific peptidase 16 Ubp-M "Nucleus;Cytosol" "SwissProt;CellAtlas" -ENSG00000156269 "ENST00000511542;ENST00000513733;ENST00000286794" "ENSP00000422022;ENSP00000286794" Q9BSU3 NAA11 84779 N-alpha-acetyltransferase 11, NatA catalytic subunit "ARD1B;ARD2;hARD2" "Golgi apparatus;Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000156411 "ENST00000286953;ENST00000554880;ENST00000555030;ENST00000414262;ENST00000553430;ENST00000554287;ENST00000557040;ENST00000553449;ENST00000554089;ENST00000554713;ENST00000557260;ENST00000554528" "ENSP00000286953;ENSP00000452133;ENSP00000452186;ENSP00000401770;ENSP00000452462;ENSP00000450894;ENSP00000451500" P56378 ATP5MJ 9556 ATP synthase membrane subunit j "6.8PL;ATP5MPL;C14orf2;MLQ;MP68" "Mitochondria;Nucleus" CellAtlas ENSG00000156413 "ENST00000318336;ENST00000524754;ENST00000527106;ENST00000286955;ENST00000592563;ENST00000531085;ENST00000531199;ENST00000532464;ENST00000528505;ENST00000526499;ENST00000591079" "ENSP00000313398;ENSP00000431708;ENSP00000432954;ENSP00000286955;ENSP00000466016;ENSP00000432161;ENSP00000436413;ENSP00000431880;ENSP00000433811" P51993 FUT6 2528 fucosyltransferase 6 "FCT3A;FLJ40754;FT1A;FucT-VI" Golgi apparatus "SwissProt;CellAtlas" ENSG00000156463 "ENST00000359120;ENST00000506591;ENST00000511217;ENST00000509286;ENST00000503848;ENST00000511705;ENST00000504522" "ENSP00000352028;ENSP00000424497" Q8TEC5 SH3RF2 153769 SH3 domain containing ring finger 2 "FLJ23654;Hepp1;POSHER;PPP1R39;RNF158" Nucleus "SwissProt;CellAtlas" @@ -2447,7 +2445,6 @@ ENSG00000183479 "ENST00000370231;ENST00000393862;ENST00000330912;ENST00000334497 ENSG00000183549 "ENST00000575584;ENST00000331849;ENST00000575070;ENST00000570305;ENST00000574748;ENST00000573920;ENST00000577024" "ENSP00000460112;ENSP00000327916;ENSP00000478073;ENSP00000461752" Q6NUN0 ACSM5 54988 acyl-CoA synthetase medium chain family member 5 FLJ20581 Mitochondria SwissProt ENSG00000183648 "ENST00000553514;ENST00000605997;ENST00000329559;ENST00000553666;ENST00000555441;ENST00000617122;ENST00000556555" "ENSP00000451090;ENSP00000475170;ENSP00000330787;ENSP00000450776;ENSP00000483888" O75438 NDUFB1 4707 NADH:ubiquinone oxidoreductase subunit B1 "CI-MNLL;MNLL" "Nucleus;Inner mitochondria" "SwissProt;CellAtlas" ENSG00000183654 "ENST00000332432;ENST00000507111;ENST00000505509" "ENSP00000333181;ENSP00000424425" A6NNE9 MARCHF11 441061 membrane associated ring-CH-type finger 11 "MARCH-XI;MARCH11;RNF226" "Cell membrane;Endoplasmic reticulum;Lysosome;Golgi apparatus" DeepLoc2 -ENSG00000183665 "ENST00000328599;ENST00000521443;ENST00000522518" "ENSP00000329858;ENSP00000429771" Q53H54 TRMT12 55039 tRNA methyltransferase 12 homolog "FLJ20772;Trm12;TYW2" "Mitochondria;Nucleus" CellAtlas ENSG00000183696 "ENST00000416681;ENST00000331803;ENST00000432131;ENST00000457596;ENST00000421046;ENST00000395564;ENST00000436673;ENST00000395560;ENST00000444999;ENST00000482015;ENST00000417464;ENST00000495446" "ENSP00000405209;ENSP00000330032;ENSP00000387607;ENSP00000408899;ENSP00000414963;ENSP00000378931;ENSP00000390118;ENSP00000378927;ENSP00000396820;ENSP00000413611" Q16831 UPP1 7378 uridine phosphorylase 1 "UDRPASE;UP;UPASE;UPP" Nucleus CellAtlas ENSG00000183747 "ENST00000574251;ENST00000570698;ENST00000573854;ENST00000576361;ENST00000417235;ENST00000575558;ENST00000219054;ENST00000575690;ENST00000571204;ENST00000574692;ENST00000571894;ENST00000396104;ENST00000572921;ENST00000572843;ENST00000576101;ENST00000576119" "ENSP00000460153;ENSP00000459451;ENSP00000460948;ENSP00000392169;ENSP00000219054;ENSP00000460349;ENSP00000460884;ENSP00000460031;ENSP00000379411" Q08AH3 ACSM2A 123876 acyl-CoA synthetase medium chain family member 2A "A-923A4.1;ACSM2;MGC150530" Mitochondria SwissProt ENSG00000183760 "ENST00000601575;ENST00000331256;ENST00000594229;ENST00000601531" "ENSP00000469048;ENSP00000327557;ENSP00000470989;ENSP00000470089" Q6ZNF0 ACP7 390928 acid phosphatase 7, tartrate resistant (putative) "FLJ16165;PAPL;PAPL1" "Extracellular;Lysosome" DeepLoc2 From 8186362a4e2b1e2a7c9e7bbca58d7d57d31d9af2 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:45:19 +0800 Subject: [PATCH 04/16] fix-GPR_curation_for_Gly_Ser_Thr_Val_Leu_Ile_metabolism (#885) * fix-GPR_curation_for_Gly_Ser_Thr_Val_Leu_Ile_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 25 +++++++++++-------------- model/genes.tsv | 1 - 2 files changed, 11 insertions(+), 15 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 00b60dbc..53204379 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -79545,7 +79545,7 @@ - MAM02181m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149124 or ENSG00000156689 or ENSG00000166840" + - gene_reaction_rule: "ENSG00000149124 or ENSG00000156689" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.13" @@ -79619,7 +79619,7 @@ - MAM02039m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149124 or ENSG00000156689 or ENSG00000166840" + - gene_reaction_rule: "ENSG00000149124" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.13" @@ -79675,7 +79675,7 @@ - MAM02530m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000161653" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.1" @@ -79730,7 +79730,7 @@ - MAM02896c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111237 or ENSG00000146733" + - gene_reaction_rule: "ENSG00000146733" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.3" @@ -79827,7 +79827,7 @@ - MAM02553c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000137106" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.79;1.1.1.81" @@ -79900,7 +79900,7 @@ - MAM02944m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000023330 or ENSG00000158578 or ENSG00000178773" + - gene_reaction_rule: "ENSG00000023330 or ENSG00000178773" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.37" @@ -80385,7 +80385,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000101323 or ENSG00000116882" + - gene_reaction_rule: "ENSG00000101323" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.3.15" @@ -82228,7 +82228,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072506 or ENSG00000106049 or ENSG00000138796" + - gene_reaction_rule: "ENSG00000072506 or ENSG00000106049" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.31;1.1.1.35" @@ -82468,7 +82468,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000179148 or ENSG00000179477 or ENSG00000188676" + - gene_reaction_rule: "ENSG00000179148 or ENSG00000179477" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.13.11.-" @@ -82487,7 +82487,7 @@ - MAM02553c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857" + - gene_reaction_rule: "ENSG00000100867 or ENSG00000109854 or ENSG00000138400 or ENSG00000145439 or ENSG00000159692 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000204228 or ENSG00000227471" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.-" @@ -271474,7 +271474,7 @@ - MAM03176c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111716 or ENSG00000134333 or ENSG00000166796 or ENSG00000166800 or ENSG00000166816 or ENSG00000171989" + - gene_reaction_rule: "ENSG00000111716 or ENSG00000134333 or ENSG00000166796 or ENSG00000166816 or ENSG00000171989" - rxnNotes: "https://www.springer.com/gp/book/9789400957800" - rxnFrom: "Recon3D" - eccodes: "1.1.1.27" @@ -306836,9 +306836,6 @@ - !!omap - id: "ENSG00000111224" - name: "PARP11" - - !!omap - - id: "ENSG00000111237" - - name: "VPS29" - !!omap - id: "ENSG00000111261" - name: "MANSC1" diff --git a/model/genes.tsv b/model/genes.tsv index 5ec73e81..c7c3f9e9 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -734,7 +734,6 @@ ENSG00000111077 "ENST00000379902;ENST00000314276;ENST00000549498;ENST00000551302 ENSG00000111144 "ENST00000228740;ENST00000537111;ENST00000552789;ENST00000553041;ENST00000413268;ENST00000548852;ENST00000547393;ENST00000548375;ENST00000547982;ENST00000552091" "ENSP00000228740;ENSP00000449958;ENSP00000395051;ENSP00000449340" P09960 LTA4H 4048 leukotriene A4 hydrolase "Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000111181 "ENST00000359674;ENST00000545058;ENST00000424061;ENST00000536824;ENST00000542825;ENST00000535498;ENST00000544782;ENST00000538272;ENST00000540094;ENST00000538580;ENST00000536116;ENST00000537793;ENST00000535347;ENST00000537826;ENST00000538424;ENST00000397296;ENST00000684302" "ENSP00000352702;ENSP00000399136;ENSP00000444268;ENSP00000439351;ENSP00000446082;ENSP00000380464;ENSP00000508194" P48065 SLC6A12 6539 solute carrier family 6 member 12 BGT-1 Cell membrane DeepLoc2 ENSG00000111224 "ENST00000416739;ENST00000427057;ENST00000458162;ENST00000228820;ENST00000476985;ENST00000453942;ENST00000450737;ENST00000447133" "ENSP00000392392;ENSP00000397058;ENSP00000399665;ENSP00000228820;ENSP00000395062;ENSP00000387481;ENSP00000405385" Q9NR21 PARP11 57097 poly(ADP-ribose) polymerase family member 11 "ARTD11;C12orf6" "Nucleus;Cytosol" "SwissProt;CellAtlas" -ENSG00000111237 "ENST00000549578;ENST00000360579;ENST00000621131;ENST00000552130;ENST00000447578;ENST00000546588;ENST00000548539;ENST00000549970;ENST00000548259;ENST00000553128;ENST00000551655;ENST00000550267" "ENSP00000447058;ENSP00000353786;ENSP00000480853;ENSP00000449954;ENSP00000400048;ENSP00000449044;ENSP00000447634" Q9UBQ0 VPS29 51699 VPS29 retromer complex component "DC15;DC7;PEP11" Cytosol "SwissProt;CellAtlas" ENSG00000111261 "ENST00000535902;ENST00000396349;ENST00000545735;ENST00000543314" "ENSP00000438205;ENSP00000379638;ENSP00000445303;ENSP00000437624" Q9H8J5 MANSC1 54682 MANSC domain containing 1 "FLJ10298;LOH12CR3" Golgi apparatus CellAtlas ENSG00000111275 "ENST00000416293;ENST00000261733;ENST00000548536;ENST00000549106;ENST00000551450" "ENSP00000403349;ENSP00000261733;ENSP00000448179;ENSP00000474669" P05091 ALDH2 217 aldehyde dehydrogenase 2 family member Mitochondria SwissProt ENSG00000111339 "ENST00000228936;ENST00000430129;ENST00000544616;ENST00000420600" "ENSP00000228936;ENSP00000412735;ENSP00000442877;ENSP00000405689" Q93070 ART4 420 ADP-ribosyltransferase 4 (inactive) (Dombrock blood group) "ARTC4;CD297;DO;DOK1" Cytosol CellAtlas From 82fa36116b52ba43538ab8d43933298652774264 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:46:16 +0800 Subject: [PATCH 05/16] Fix-GPR curation for Galactose, Fructose and mannose metabolism (#886) * fix-GPR curation for Galactose, Fructose and mannose metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 30 ++++++++++++------------------ model/genes.tsv | 2 -- 2 files changed, 12 insertions(+), 20 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 53204379..63873688 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -68983,7 +68983,7 @@ - MAM02945e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000090402 or ENSG00000171298 or ENSG00000214013 or ENSG00000257335" + - gene_reaction_rule: "ENSG00000090402 or ENSG00000214013 or ENSG00000257335" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.10;3.2.1.20;3.2.1.48" @@ -69038,7 +69038,7 @@ - MAM02040e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000102393 or ENSG00000170266 or ENSG00000241343" + - gene_reaction_rule: "ENSG00000102393 or ENSG00000170266" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.22;3.2.1.23" @@ -69117,7 +69117,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.3" - - references: "PMID:33715524" + - references: "PMID:33715524;PMID:246961;PMID:19158351" - subsystem: - "Galactose metabolism" - confidence_score: 0 @@ -69167,7 +69167,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085662 or ENSG00000198074" + - gene_reaction_rule: "ENSG00000085662" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.21" @@ -69281,7 +69281,7 @@ - MAM02555c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085662 or ENSG00000198074" + - gene_reaction_rule: "ENSG00000085662" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.21" @@ -69300,7 +69300,7 @@ - MAM02917c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" + - gene_reaction_rule: "ENSG00000116199" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.-" @@ -69319,7 +69319,7 @@ - MAM02039c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" + - gene_reaction_rule: "ENSG00000167363 or ENSG00000172456" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.-" @@ -69357,7 +69357,7 @@ - MAM02454c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" + - gene_reaction_rule: "ENSG00000116199" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.-" @@ -69406,7 +69406,7 @@ - MAM02455c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100413 or ENSG00000100417 or ENSG00000140650" + - gene_reaction_rule: "ENSG00000100417 or ENSG00000140650" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "5.4.2.8" @@ -69425,7 +69425,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000164068 or ENSG00000173540" + - gene_reaction_rule: "ENSG00000173540" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.7.22;2.7.7.13" @@ -69499,7 +69499,7 @@ - MAM02759c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116783 or ENSG00000254685" + - gene_reaction_rule: "ENSG00000254685" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.7.30" @@ -223305,7 +223305,7 @@ - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "2.7.1.3" - - references: "PMID:33715524" + - references: "PMID:33715524;PMID:2469615;PMID:19158351" - subsystem: - "Galactose metabolism" - confidence_score: 0 @@ -307292,9 +307292,6 @@ - !!omap - id: "ENSG00000116771" - name: "AGMAT" - - !!omap - - id: "ENSG00000116783" - - name: "TNNI3K" - !!omap - id: "ENSG00000116791" - name: "CRYZ" @@ -313025,9 +313022,6 @@ - !!omap - id: "ENSG00000241119" - name: "UGT1A9" - - !!omap - - id: "ENSG00000241343" - - name: "RPL36A" - !!omap - id: "ENSG00000241360" - name: "PDXP" diff --git a/model/genes.tsv b/model/genes.tsv index c7c3f9e9..2580393e 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -884,7 +884,6 @@ ENSG00000116745 ENST00000262340 ENSP00000262340 Q16518 RPE65 6121 retinoid isome ENSG00000116748 "ENST00000637080;ENST00000520113;ENST00000369538;ENST00000639274;ENST00000639077;ENST00000638214;ENST00000485564" "ENSP00000489753;ENSP00000430075;ENSP00000358551" P23109 AMPD1 270 adenosine monophosphate deaminase 1 "MAD;MADA" "Cytosol;Nucleus" DeepLoc2 ENSG00000116761 "ENST00000411986;ENST00000370938;ENST00000464926;ENST00000346806;ENST00000482383" "ENSP00000413407;ENSP00000359976;ENSP00000311554" P32929 CTH 1491 cystathionine gamma-lyase Cytosol SwissProt ENSG00000116771 ENST00000375826 ENSP00000364986 Q9BSE5 AGMAT 79814 agmatinase FLJ23384 Mitochondria DeepLoc2 -ENSG00000116783 "ENST00000326637;ENST00000530184;ENST00000497284;ENST00000526236;ENST00000534020;ENST00000525480;ENST00000370889;ENST00000465473" "ENSP00000322251;ENSP00000431465;ENSP00000434975;ENSP00000433550" Q59H18 TNNI3K 51086 TNNI3 interacting kinase CARK "Cytosol;Nucleus" SwissProt ENSG00000116791 "ENST00000370872;ENST00000340866;ENST00000492102;ENST00000417775;ENST00000370871;ENST00000370870;ENST00000441120" "ENSP00000359909;ENSP00000339399;ENSP00000399805;ENSP00000359908;ENSP00000359907;ENSP00000404289" Q08257 CRYZ 1429 crystallin zeta Cytosol "SwissProt;CellAtlas" ENSG00000116882 "ENST00000457318;ENST00000361035;ENST00000325945;ENST00000482991;ENST00000622548" "ENSP00000393955;ENSP00000354314;ENSP00000316339;ENSP00000483507" Q9NYQ3 HAO2 51179 hydroxyacid oxidase 2 "GIG16;HAOX2" "Peroxisome;Cytosol" "SwissProt;CellAtlas" ENSG00000116906 "ENST00000436239;ENST00000366647;ENST00000416000;ENST00000644483;ENST00000492459;ENST00000469332" "ENSP00000402811;ENSP00000355607;ENSP00000411640;ENSP00000496537" O15228 GNPAT 8443 glyceronephosphate O-acyltransferase "DAP-AT;DAPAT;DHAPAT" Peroxisome SwissProt @@ -2778,7 +2777,6 @@ ENSG00000240857 "ENST00000381249;ENST00000468071" ENSP00000370648 Q9HBH5 RDH14 5 ENSG00000240891 "ENST00000636933;ENST00000393934;ENST00000477665;ENST00000468174;ENST00000474484" "ENSP00000490816;ENSP00000377511;ENSP00000420686" Q0VAA5 PLCXD2 257068 phosphatidylinositol specific phospholipase C X domain containing 2 FLJ31579 Nucleus CellAtlas ENSG00000240972 "ENST00000215754;ENST00000465752;ENST00000498385" ENSP00000215754 P14174 MIF 4282 macrophage migration inhibitory factor "GIF;GLIF" "Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000241119 ENST00000354728 ENSP00000346768 O60656 UGT1A9 54600 UDP glucuronosyltransferase family 1 member A9 "HLUGP4;LUGP4;UGT1AI" Endoplasmic reticulum SwissProt -ENSG00000241343 "ENST00000427805;ENST00000614077;ENST00000392994;ENST00000491851;ENST00000465340;ENST00000553110;ENST00000372849;ENST00000465744;ENST00000471855;ENST00000489407" "ENSP00000404375;ENSP00000483017;ENSP00000397659;ENSP00000446503;ENSP00000361940;ENSP00000473451" P83881 RPL36A 6173 ribosomal protein L36a "L36A;RPL44" "Endoplasmic reticulum;Cytosol" "SwissProt;CellAtlas" ENSG00000241360 "ENST00000215904;ENST00000403251" "ENSP00000215904;ENSP00000385336" Q96GD0 PDXP 57026 pyridoxal phosphatase "CIN;dJ37E16.5;FLJ32703" Cytosol SwissProt ENSG00000241404 "ENST00000333845;ENST00000395512;ENST00000432129;ENST00000466239;ENST00000482938;ENST00000489721" "ENSP00000333380;ENSP00000378888;ENSP00000401694" Q99944 EGFL8 80864 EGF like domain multiple 8 "C6orf8;NG3" Nucleus CellAtlas ENSG00000241468 "ENST00000466753;ENST00000414062;ENST00000449683;ENST00000491560;ENST00000359832;ENST00000292475;ENST00000488775;ENST00000394186;ENST00000481899;ENST00000523680;ENST00000485011;ENST00000524321" "ENSP00000412149;ENSP00000407540;ENSP00000352890;ENSP00000292475;ENSP00000418197;ENSP00000377740;ENSP00000430398" P56134 ATP5MF 9551 ATP synthase membrane subunit f "ATP5J2;ATP5JL" "Nucleus;Inner mitochondria" "SwissProt;CellAtlas" From c0f3a66393c0aad09345e7540b490e5e8c185bc2 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:47:44 +0800 Subject: [PATCH 06/16] Fix-GPR curation for Purine metabolism (#898) * fix-GPR_curation_for_Purine_metabolism * chore: add macaw test result --------- Co-authored-by: Eduard Kerkhoven Co-authored-by: edkerk --- model/Human-GEM.yml | 46 ++++++++++++++++++++++----------------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 63873688..4e54774f 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -71448,7 +71448,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000054179 or ENSG00000138185 or ENSG00000168032 or ENSG00000171302 or ENSG00000187097 or ENSG00000188833 or ENSG00000197217 or ENSG00000197586" + - gene_reaction_rule: "ENSG00000054179 or ENSG00000138185 or ENSG00000168032 or ENSG00000171302 or ENSG00000187097 or ENSG00000188833 or ENSG00000197586" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.6.1.5;3.6.1.6" @@ -71465,7 +71465,7 @@ - MAM02759c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000061918 and ENSG00000164116) or ENSG00000070019 or ENSG00000078295 or ENSG00000101890 or ENSG00000121281 or ENSG00000129467 or ENSG00000132518 or ENSG00000138031 or ENSG00000143199 or ENSG00000152402 or ENSG00000155897 or ENSG00000159899 or ENSG00000162104 or ENSG00000164742 or ENSG00000169418 or ENSG00000173175 or ENSG00000174233" + - gene_reaction_rule: "(ENSG00000061918 and ENSG00000164116) or ENSG00000078295 or ENSG00000121281 or ENSG00000129467 or ENSG00000138031 or ENSG00000143199 or ENSG00000155897 or ENSG00000159899 or ENSG00000162104 or ENSG00000164742 or ENSG00000173175 or ENSG00000174233" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.6.1.1;4.6.1.2" @@ -71517,7 +71517,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000125458 or ENSG00000135318 or ENSG00000146587 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -71535,7 +71535,7 @@ - MAM02751e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -71553,7 +71553,7 @@ - MAM02751m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -71590,7 +71590,7 @@ - MAM02040c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268" + - gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.4.17" @@ -71625,7 +71625,7 @@ - MAM02759c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000061918 and ENSG00000164116) or ENSG00000070019 or ENSG00000078295 or ENSG00000101890 or ENSG00000121281 or ENSG00000129467 or ENSG00000132518 or ENSG00000138031 or ENSG00000143199 or ENSG00000152402 or ENSG00000155897 or ENSG00000159899 or ENSG00000162104 or ENSG00000164742 or ENSG00000169418 or ENSG00000173175 or ENSG00000174233" + - gene_reaction_rule: "(ENSG00000061918 and ENSG00000164116) or ENSG00000070019 or ENSG00000078295 or ENSG00000101890 or ENSG00000121281 or ENSG00000132518 or ENSG00000138031 or ENSG00000143199 or ENSG00000152402 or ENSG00000155897 or ENSG00000159899 or ENSG00000169418" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.6.1.1;4.6.1.2" @@ -71724,7 +71724,7 @@ - MAM02040c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000065989 or ENSG00000073417 or ENSG00000095464 or ENSG00000105650 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000184588 or ENSG00000185527 or ENSG00000186642 or ENSG00000205268" + - gene_reaction_rule: "ENSG00000073417 or ENSG00000095464 or ENSG00000112541 or ENSG00000113231 or ENSG00000113448 or ENSG00000115252 or ENSG00000123360 or ENSG00000128655 or ENSG00000132915 or ENSG00000133256 or ENSG00000138735 or ENSG00000139053 or ENSG00000152270 or ENSG00000154678 or ENSG00000160191 or ENSG00000171408 or ENSG00000172572 or ENSG00000185527 or ENSG00000186642" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.4.17;3.1.4.35" @@ -71834,7 +71834,7 @@ - MAM02759c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125877" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.6.1.19;3.6.1.8" @@ -71927,7 +71927,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000125458 or ENSG00000135318 or ENSG00000146587 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -72002,7 +72002,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -72020,7 +72020,7 @@ - MAM02751e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -72096,7 +72096,7 @@ - MAM01639c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000004455 or ENSG00000072778 or ENSG00000085231 or ENSG00000087008 or ENSG00000106992 or ENSG00000117054 or ENSG00000140057 or ENSG00000147853 or ENSG00000151498 or ENSG00000154027 or ENSG00000155085 or ENSG00000162433 or ENSG00000165695 or ENSG00000177646" + - gene_reaction_rule: "ENSG00000004455 or ENSG00000085231 or ENSG00000106992 or ENSG00000140057 or ENSG00000147853 or ENSG00000154027 or ENSG00000155085 or ENSG00000162433 or ENSG00000165695 or ENSG00000177646" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.11;2.7.4.3" @@ -72265,7 +72265,7 @@ - MAM02193c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156510 or ENSG00000156515 or ENSG00000159399 or ENSG00000160883" + - gene_reaction_rule: "ENSG00000156515 or ENSG00000159399" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.1" @@ -72284,7 +72284,7 @@ - MAM02039c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156510 or ENSG00000156515 or ENSG00000159399 or ENSG00000160883" + - gene_reaction_rule: "ENSG00000156510 or ENSG00000156515 or ENSG00000159399" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.1" @@ -72415,7 +72415,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -72603,7 +72603,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -72789,7 +72789,7 @@ - MAM03150c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -72927,7 +72927,7 @@ - MAM02872c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100354 or ENSG00000239900" + - gene_reaction_rule: "ENSG00000239900" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.3.2.2" @@ -73038,7 +73038,7 @@ - MAM03121e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000167419" + - gene_reaction_rule: "ENSG00000121053 or ENSG00000130508 or ENSG00000167419" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.11.1.7" @@ -73257,7 +73257,7 @@ - MAM01642c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" + - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.6" @@ -73275,7 +73275,7 @@ - MAM02193c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" + - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.6" @@ -217612,7 +217612,7 @@ - MAM03200l: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000102575 or ENSG00000134575 or ENSG00000162836" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000102575 or ENSG00000134575" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "3.1.3.2" From 8cc91738a83f901dcc74f224b902ba356a726c2a Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:49:09 +0800 Subject: [PATCH 07/16] Fix-Phe, Tyr and Trp biosynthesis and Porphyrin metabolism (#899) * Fix-GPR curation for Phe, Tyr and Trp biosynthesis and Porphyrin metabolism * chore: add macaw test result * chore: add gene essentiality test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven Co-authored-by: edkerk --- model/Human-GEM.yml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 4e54774f..034fb88c 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -83612,7 +83612,7 @@ - MAM03136c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.5" @@ -83632,7 +83632,7 @@ - MAM03136c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.5" @@ -83733,7 +83733,7 @@ - MAM02555c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.5" @@ -83771,7 +83771,7 @@ - MAM02553c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1" @@ -83849,7 +83849,7 @@ - MAM02553c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.5" @@ -83869,7 +83869,7 @@ - MAM02555c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.5" @@ -83986,7 +83986,7 @@ - MAM02555c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.5" @@ -84307,7 +84307,7 @@ - MAM02555c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.5" @@ -84491,7 +84491,7 @@ - MAM02041c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000167419" + - gene_reaction_rule: "ENSG00000121053 or ENSG00000167419" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.11.1.7" @@ -84527,7 +84527,7 @@ - MAM02041c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000005381 or ENSG00000115705 or ENSG00000117592 or ENSG00000121053 or ENSG00000167419" + - gene_reaction_rule: "ENSG00000005381 or ENSG00000115705 or ENSG00000121053 or ENSG00000167419" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.11.1.7;1.11.1.8;1.11.2.2" @@ -84765,7 +84765,7 @@ - MAM02682c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000070614 or ENSG00000111962 or ENSG00000115526 or ENSG00000124302 or ENSG00000130540 or ENSG00000135702 or ENSG00000136720 or ENSG00000138653 or ENSG00000140835 or ENSG00000147119 or ENSG00000153936 or ENSG00000154080 or ENSG00000154252 or ENSG00000164100 or ENSG00000166507 or ENSG00000171004 or ENSG00000173597 or ENSG00000175040 or ENSG00000175229 or ENSG00000183196 or ENSG00000185352 or ENSG00000197093 or ENSG00000198075 or ENSG00000198203" + - gene_reaction_rule: "ENSG00000070614 or ENSG00000111962 or ENSG00000115526 or ENSG00000130540 or ENSG00000147119 or ENSG00000153936 or ENSG00000154080 or ENSG00000154252 or ENSG00000164100 or ENSG00000173597 or ENSG00000185352 or ENSG00000197093 or ENSG00000198075 or ENSG00000198203" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -85410,7 +85410,7 @@ - MAM02724c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117592 or ENSG00000121053 or ENSG00000130508 or ENSG00000167419" + - gene_reaction_rule: "ENSG00000121053" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.11.1.7" @@ -229667,7 +229667,7 @@ - MAM02751m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000151093" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "3.1.3.66" From 0fc5ae30e11f7f09cafe497aeb3f91c7f0e88f8f Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:50:56 +0800 Subject: [PATCH 08/16] Fix: GPR curation for Inositol phosphate metabolism (#905) * fix-GPR_curation_for_Inositol_phosphate_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 034fb88c..bf6a70de 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -150543,7 +150543,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000104331 or ENSG00000133731 or ENSG00000141401" + - gene_reaction_rule: "ENSG00000133731 or ENSG00000141401" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.25" @@ -150617,7 +150617,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163082 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000198881 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920" + - gene_reaction_rule: "ENSG00000003987 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000198881 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.-" @@ -150654,7 +150654,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163082 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920" + - gene_reaction_rule: "ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000211456" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.-" @@ -150838,7 +150838,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163082 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000198881 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920" + - gene_reaction_rule: "ENSG00000003987 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000165458 or ENSG00000198825 or ENSG00000198881 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.-" @@ -150929,7 +150929,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000104331 or ENSG00000133731 or ENSG00000141401" + - gene_reaction_rule: "ENSG00000133731 or ENSG00000141401" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.25" @@ -151095,7 +151095,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000104331 or ENSG00000133731 or ENSG00000141401" + - gene_reaction_rule: "ENSG00000133731 or ENSG00000141401" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.25" @@ -151373,7 +151373,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163082 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920" + - gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.-" @@ -151411,7 +151411,7 @@ - MAM02735c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000107242 or ENSG00000143398 or ENSG00000167103 or ENSG00000186111" + - gene_reaction_rule: "ENSG00000143398 or ENSG00000167103 or ENSG00000186111" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.68" @@ -151725,7 +151725,7 @@ - MAM02734n: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000107242 or ENSG00000143398 or ENSG00000167103 or ENSG00000186111" + - gene_reaction_rule: "ENSG00000107242 or ENSG00000143398 or ENSG00000167103" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" From 7ebff3fb5c695438a9e4202046b36e14dca8b42e Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:52:05 +0800 Subject: [PATCH 09/16] =?UTF-8?q?fix-GPR=5Fcuration=5Ffor=5FSerotonin=20an?= =?UTF-8?q?d=20melatonin=20biosynthesis=20and=20Keratan=E2=80=A6=20(#907)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * fix-GPR_curation_for_Serotonin and melatonin biosynthesis and Keratan sulfate biosynthesis * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- data/testResults/README.md | 2 +- model/Human-GEM.yml | 64 +++++++++++++++++++------------------- 2 files changed, 33 insertions(+), 33 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 78746c32..3ed4bf13 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #928** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #907** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index bf6a70de..1c10bcba 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -141463,7 +141463,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141501,7 +141501,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141520,7 +141520,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141558,7 +141558,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141577,7 +141577,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141615,7 +141615,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141634,7 +141634,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141672,7 +141672,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141691,7 +141691,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141729,7 +141729,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141748,7 +141748,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141786,7 +141786,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141805,7 +141805,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141843,7 +141843,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141862,7 +141862,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141900,7 +141900,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141919,7 +141919,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141957,7 +141957,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141976,7 +141976,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -142014,7 +142014,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142033,7 +142033,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -142071,7 +142071,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142185,7 +142185,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142223,7 +142223,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142242,7 +142242,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -142280,7 +142280,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142394,7 +142394,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142432,7 +142432,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142451,7 +142451,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -142489,7 +142489,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142508,7 +142508,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -156497,7 +156497,7 @@ - MAM02949c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000070614 or ENSG00000111962 or ENSG00000115526 or ENSG00000124302 or ENSG00000130540 or ENSG00000135702 or ENSG00000136720 or ENSG00000138653 or ENSG00000140835 or ENSG00000147119 or ENSG00000153936 or ENSG00000154080 or ENSG00000154252 or ENSG00000164100 or ENSG00000166507 or ENSG00000171004 or ENSG00000173597 or ENSG00000175040 or ENSG00000175229 or ENSG00000183196 or ENSG00000185352 or ENSG00000197093 or ENSG00000198075 or ENSG00000198203 or ENSG00000261052" + - gene_reaction_rule: "ENSG00000070614 or ENSG00000115526 or ENSG00000130540 or ENSG00000135702 or ENSG00000138653 or ENSG00000147119 or ENSG00000153936 or ENSG00000154080 or ENSG00000173597 or ENSG00000197093 or ENSG00000198203 or ENSG00000261052" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" From 6e5a5f687484d9b83dc8887ab63f95465a28a947 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:53:19 +0800 Subject: [PATCH 10/16] Fix: GPR curation for retinol metabolism and riboflavin metabolism (#914) * fix-GPR_curation_for_Retinol_metabolism-and-Riboflavin_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 1c10bcba..baeb2cb2 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -154694,7 +154694,7 @@ - MAM02834c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000025423 or ENSG00000135437 or ENSG00000147576 or ENSG00000170786 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000025423 or ENSG00000135437 or ENSG00000170786 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1;1.1.1.105" @@ -154732,7 +154732,7 @@ - MAM02834r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000025423 or ENSG00000135437 or ENSG00000147576 or ENSG00000170786 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000025423 or ENSG00000135437 or ENSG00000170786 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1;1.1.1.105" @@ -154771,7 +154771,7 @@ - MAM02838c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000062282 or ENSG00000114113 or ENSG00000114115 or ENSG00000121207 or ENSG00000147160 or ENSG00000185000 or ENSG00000204195" + - gene_reaction_rule: "ENSG00000062282 or ENSG00000114113 or ENSG00000114115 or ENSG00000121207 or ENSG00000147160 or ENSG00000185000" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.135;2.3.1.75" @@ -154828,7 +154828,7 @@ - MAM02553c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000025423 or ENSG00000135437 or ENSG00000139547 or ENSG00000140522 or ENSG00000157326 or ENSG00000170786 or ENSG00000187630 or ENSG00000265203" + - gene_reaction_rule: "ENSG00000025423 or ENSG00000135437 or ENSG00000139547 or ENSG00000140522 or ENSG00000157326 or ENSG00000187630 or ENSG00000265203" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.105" @@ -154863,7 +154863,7 @@ - MAM02834c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000163684 or ENSG00000244486" + - gene_reaction_rule: "ENSG00000244486" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.-" @@ -155195,7 +155195,7 @@ - MAM02833c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" @@ -155216,7 +155216,7 @@ - MAM02833r: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" + - gene_reaction_rule: "ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.14.14.1" @@ -155264,7 +155264,7 @@ - MAM02833c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000134184" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -155429,7 +155429,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857" + - gene_reaction_rule: "ENSG00000109854 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.-" @@ -156182,7 +156182,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000025423 or ENSG00000135437 or ENSG00000139547 or ENSG00000140522 or ENSG00000157326 or ENSG00000170786 or ENSG00000187630 or ENSG00000265203" + - gene_reaction_rule: "ENSG00000025423 or ENSG00000135437 or ENSG00000139547 or ENSG00000140522 or ENSG00000157326 or ENSG00000187630 or ENSG00000265203" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.105" @@ -156310,7 +156310,7 @@ - MAM02842c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000102575 or ENSG00000142513 or ENSG00000155893 or ENSG00000162836 or ENSG00000183760" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000142513 or ENSG00000183760" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.2" @@ -303422,7 +303422,7 @@ - MAM02040x: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000112874" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "" - eccodes: "" From 655b7f44d3430166c32d43192a2ba4a46eb8aa4b Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:54:16 +0800 Subject: [PATCH 11/16] fix-GPR curation for PPP, TCA and Pyruvate metabolism (#915) * fix-GPR_curation_for_PPP_TCA_Pyruvate_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index baeb2cb2..e247eeab 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -70005,7 +70005,7 @@ - MAM02819c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000166816 or ENSG00000182224" + - gene_reaction_rule: "ENSG00000166816" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.2.4" @@ -70297,7 +70297,7 @@ - MAM02553c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1" @@ -70317,7 +70317,7 @@ - MAM02553c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000072210 or ENSG00000108602 or ENSG00000132746 or ENSG00000143149 or ENSG00000164904 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000072210 or ENSG00000108602 or ENSG00000132746 or ENSG00000143149 or ENSG00000164904" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.4;1.2.1.5" @@ -70357,7 +70357,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072210 or ENSG00000111275 or ENSG00000137124 or ENSG00000143149 or ENSG00000164904" + - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000143149 or ENSG00000164904" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.3" @@ -70376,7 +70376,7 @@ - MAM02771c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -70395,7 +70395,7 @@ - MAM02771c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -70471,7 +70471,7 @@ - MAM02819c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000166816 or ENSG00000182224" + - gene_reaction_rule: "ENSG00000182224" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.2.4" @@ -70488,11 +70488,11 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000148090" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PMID: 25709564" - subsystem: - "Pyruvate metabolism" - confidence_score: 0 @@ -71282,7 +71282,7 @@ - MAM02884c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067057 or ENSG00000141959 or ENSG00000152556" + - gene_reaction_rule: "ENSG00000067057 or ENSG00000141959" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.11" @@ -71320,7 +71320,7 @@ - MAM03166c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000138030" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.3" @@ -71429,7 +71429,7 @@ - MAM02553r: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000049239 or ENSG00000130313" + - gene_reaction_rule: "ENSG00000049239" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.1.31" @@ -94150,7 +94150,7 @@ - MAM02661x: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000101323 or ENSG00000116882" + - gene_reaction_rule: "ENSG00000101323" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.3.15" @@ -94168,7 +94168,7 @@ - MAM02007x: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000101323 or ENSG00000116882" + - gene_reaction_rule: "ENSG00000101323" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.3.15" @@ -94242,7 +94242,7 @@ - MAM02553c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000072210 or ENSG00000108602 or ENSG00000132746 or ENSG00000143149 or ENSG00000164904 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000072210 or ENSG00000108602 or ENSG00000132746 or ENSG00000143149 or ENSG00000164904" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.4;1.2.1.5" @@ -94280,7 +94280,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072210 or ENSG00000111275 or ENSG00000137124 or ENSG00000143149 or ENSG00000164904" + - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000143149 or ENSG00000164904" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.3" @@ -302590,7 +302590,7 @@ - MAM02884c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000130957 or ENSG00000165140" + - gene_reaction_rule: "" - rxnNotes: "https://doi.org/10.1007/BF02702726" - rxnFrom: "" - eccodes: "3.1.3.11" From 778e765b988891f8c73f069ca35b7e497aea97da Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:55:26 +0800 Subject: [PATCH 12/16] Fix: GPR curation for Carnitine shuttle (#923) * fix-GPR_curation_for_Carnitine_shuttle * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 123 +++++++++++++++++++++----------------------- model/genes.tsv | 1 - 2 files changed, 60 insertions(+), 64 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e247eeab..e8e3838f 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -110881,7 +110881,7 @@ - MAM02348c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.21" @@ -111080,7 +111080,7 @@ - MAM02634m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000178537 or ENSG00000197119" + - gene_reaction_rule: "ENSG00000178537" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111116,7 +111116,7 @@ - MAM02657m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000178537 or ENSG00000197119" + - gene_reaction_rule: "ENSG00000178537" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111152,7 +111152,7 @@ - MAM02443m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111188,7 +111188,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111224,7 +111224,7 @@ - MAM03049m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111260,7 +111260,7 @@ - MAM02973m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111296,7 +111296,7 @@ - MAM02974m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111332,7 +111332,7 @@ - MAM02975m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111368,7 +111368,7 @@ - MAM02976m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111404,7 +111404,7 @@ - MAM02688m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111440,11 +111440,11 @@ - MAM02411m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "PMID:14598172;PMID:18406340;PMID:6361812;PMID:8132483;PMID:1735445;PMID:1988962;PMID:2351134;PMID:2355017;PMID:7892212PMID:9399886" + - references: "PMID:14598172;PMID:18406340;PMID:6361812;PMID:8132483;PMID:1735445;PMID:1988962;PMID:2351134;PMID:2355017;PMID:7892212;PMID:9399886;PubMed:10215651;PubMed:15107849;PubMed:16729965" - subsystem: - "Carnitine shuttle (mitochondrial)" - confidence_score: 0 @@ -111476,7 +111476,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111512,7 +111512,7 @@ - MAM02676m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111548,7 +111548,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111584,7 +111584,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111620,7 +111620,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111656,11 +111656,11 @@ - MAM02940m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PubMed:10215651;PubMed:15107849;PubMed:16729965" - subsystem: - "Carnitine shuttle (mitochondrial)" - confidence_score: 0 @@ -111692,7 +111692,7 @@ - MAM02639m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111728,7 +111728,7 @@ - MAM02640m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111764,7 +111764,7 @@ - MAM02410m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111800,7 +111800,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111836,7 +111836,7 @@ - MAM02638m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111872,7 +111872,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111908,7 +111908,7 @@ - MAM02611m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111944,7 +111944,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -111980,7 +111980,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112016,7 +112016,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112052,7 +112052,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112088,7 +112088,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112124,7 +112124,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112160,7 +112160,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112196,7 +112196,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112232,7 +112232,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112268,7 +112268,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112304,7 +112304,7 @@ - MAM02637m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112340,7 +112340,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112376,7 +112376,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112412,7 +112412,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112448,7 +112448,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112484,7 +112484,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112520,11 +112520,11 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PubMed:10215651;PubMed:15107849;PubMed:16729965" - subsystem: - "Carnitine shuttle (mitochondrial)" - confidence_score: 0 @@ -112556,7 +112556,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112592,7 +112592,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112628,7 +112628,7 @@ - MAM02388m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112664,7 +112664,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112700,7 +112700,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112736,7 +112736,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112772,7 +112772,7 @@ - MAM02636m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112808,7 +112808,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112844,7 +112844,7 @@ - MAM02348m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112880,7 +112880,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -112917,7 +112917,7 @@ - MAM02348m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197119 or ENSG00000197208" + - gene_reaction_rule: "ENSG00000149742 or ENSG00000175003 or ENSG00000178537 or ENSG00000197208" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -113097,7 +113097,7 @@ - MAM02409x: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000178537 or ENSG00000197119" + - gene_reaction_rule: "ENSG00000178537" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -113133,7 +113133,7 @@ - MAM02657x: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000178537 or ENSG00000197119" + - gene_reaction_rule: "ENSG00000178537" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -113205,7 +113205,7 @@ - MAM02443r: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000178537 or ENSG00000197119" + - gene_reaction_rule: "ENSG00000178537" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -115366,7 +115366,7 @@ - MAM02348c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.21" @@ -312425,9 +312425,6 @@ - !!omap - id: "ENSG00000197093" - name: "GAL3ST4" - - !!omap - - id: "ENSG00000197119" - - name: "SLC25A29" - !!omap - id: "ENSG00000197121" - name: "PGAP1" diff --git a/model/genes.tsv b/model/genes.tsv index 2580393e..70025866 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2578,7 +2578,6 @@ ENSG00000196839 "ENST00000464097;ENST00000372874;ENST00000536532;ENST00000492931 ENSG00000196950 "ENST00000458054;ENST00000409086;ENST00000444421;ENST00000359634;ENST00000430412;ENST00000412905;ENST00000464301;ENST00000418005;ENST00000465851" "ENSP00000389640;ENSP00000386766;ENSP00000394469;ENSP00000352655;ENSP00000394995;ENSP00000406590;ENSP00000409272" Q9ULF5 SLC39A10 57181 solute carrier family 39 member 10 "DKFZp564L2123;FLJ90515;KIAA1265" "Cytosol;Nucleus" CellAtlas ENSG00000196968 "ENST00000372841;ENST00000394790;ENST00000465695;ENST00000489264" "ENSP00000361932;ENSP00000378270" Q495W5 FUT11 170384 fucosyltransferase 11 MGC33202 "Golgi apparatus;Nucleus" "SwissProt;CellAtlas" ENSG00000197093 "ENST00000413800;ENST00000495882;ENST00000360039;ENST00000423751;ENST00000411994;ENST00000498000;ENST00000482469;ENST00000460995" "ENSP00000400451;ENSP00000353142;ENSP00000399066;ENSP00000414733;ENSP00000488586;ENSP00000487594;ENSP00000488800" Q96RP7 GAL3ST4 79690 galactose-3-O-sulfotransferase 4 FLJ12116 "Golgi apparatus;Nucleus;Cytosol" "SwissProt;CellAtlas" -ENSG00000197119 "ENST00000359232;ENST00000554912;ENST00000392908;ENST00000556505;ENST00000555927;ENST00000554224;ENST00000556715;ENST00000554291;ENST00000554060;ENST00000556868;ENST00000555475;ENST00000553359;ENST00000556873;ENST00000553574;ENST00000555051;ENST00000555949;ENST00000557438;ENST00000555888;ENST00000556201;ENST00000556844" "ENSP00000352167;ENSP00000450913;ENSP00000376640;ENSP00000452446;ENSP00000452078;ENSP00000451573;ENSP00000451952;ENSP00000452324;ENSP00000451644;ENSP00000451808" Q8N8R3 SLC25A29 123096 solute carrier family 25 member 29 "C14orf69;FLJ38975" Inner mitochondria SwissProt ENSG00000197121 "ENST00000354764;ENST00000423035;ENST00000422444;ENST00000459896;ENST00000470179;ENST00000409475;ENST00000476250;ENST00000482051;ENST00000409188;ENST00000374738;ENST00000485830" "ENSP00000346809;ENSP00000415405;ENSP00000390555;ENSP00000387028;ENSP00000386802;ENSP00000363870" Q75T13 PGAP1 80055 post-GPI attachment to proteins inositol deacylase 1 "Bst1;FLJ12377;SPG67" Endoplasmic reticulum SwissProt ENSG00000197142 "ENST00000354655;ENST00000393081;ENST00000433418;ENST00000356116;ENST00000354273;ENST00000495539;ENST00000467340;ENST00000496328" "ENSP00000346680;ENSP00000376796;ENSP00000403647;ENSP00000348429;ENSP00000346223;ENSP00000507158" Q9ULC5 ACSL5 51703 acyl-CoA synthetase long chain family member 5 "ACS2;ACS5;FACL5" "Endoplasmic reticulum;Mitochondria;Nucleus" "SwissProt;CellAtlas" ENSG00000197165 "ENST00000534108;ENST00000533150;ENST00000335715;ENST00000395630;ENST00000526384" "ENSP00000433075;ENSP00000435271;ENSP00000338742;ENSP00000378992;ENSP00000435358" P50226 SULT1A2 6799 sulfotransferase family 1A member 2 "HAST4;STP2" Cytosol SwissProt From 035e08e202995a1d9d802d3a711ed1568b9ae910 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:56:16 +0800 Subject: [PATCH 13/16] Fix-GPR curation for EMP and Pentose and glucuronate interconversions (#924) * Fix-GPR_curation_for_EMP-Pentose_and_glucuronate_interconversions * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e8e3838f..79c418c4 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -67661,7 +67661,7 @@ - MAM02553c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1;1.1.1.71" @@ -67816,7 +67816,7 @@ - MAM02555c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.5" @@ -67930,7 +67930,7 @@ - MAM02819c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000180011" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.49" @@ -68265,7 +68265,7 @@ - MAM02578r: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000131482 or ENSG00000141349 or ENSG00000152254" + - gene_reaction_rule: "ENSG00000152254" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.9" @@ -69628,7 +69628,7 @@ - MAM03155c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000115425 or ENSG00000116353" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.15" @@ -69647,7 +69647,7 @@ - MAM03155c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085662 or ENSG00000198074" + - gene_reaction_rule: "ENSG00000085662" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.21" @@ -69873,7 +69873,7 @@ - MAM03109c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000115652" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.1.35" From d3472ad996609fd7d647b7cf6b9b91cc78f294a6 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:59:08 +0800 Subject: [PATCH 14/16] Fix: GPR curation of Bile_acid_biosynthesis/recycling (#930) * Fix: GPR curation of Bile_acid_biosynthesis/recycling * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 48 ++++++++++++++++++++++----------------------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 79c418c4..5588d829 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -144641,7 +144641,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825" + - gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000184343 or ENSG00000185825" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -145259,7 +145259,7 @@ - MAM02040x: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000097021 or ENSG00000119673 or ENSG00000136881 or ENSG00000177465 or ENSG00000184227 or ENSG00000205669" + - gene_reaction_rule: "ENSG00000184227 or ENSG00000097021 or ENSG00000136881" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.2.2" @@ -145294,7 +145294,7 @@ - MAM02040c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000097021 or ENSG00000119673 or ENSG00000136881 or ENSG00000177465 or ENSG00000184227 or ENSG00000205669" + - gene_reaction_rule: "ENSG00000177465 or ENSG00000101473 or ENSG00000136881" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.2.2" @@ -145384,7 +145384,7 @@ - MAM02759c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000083807 or ENSG00000140284" + - gene_reaction_rule: "ENSG00000083807" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "6.2.1.7" @@ -146262,7 +146262,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000138135" + - gene_reaction_rule: "ENSG00000135929" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.14.99.38" @@ -146602,7 +146602,7 @@ - MAM02555r: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857" + - gene_reaction_rule: "ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.-" @@ -147060,7 +147060,7 @@ - MAM02157c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000128683 or ENSG00000136750 or ENSG00000139631" + - gene_reaction_rule: "ENSG00000128683 or ENSG00000139631" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.1.15;4.1.1.29" @@ -147152,7 +147152,7 @@ - MAM02961c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000128683 or ENSG00000136750 or ENSG00000139631" + - gene_reaction_rule: "ENSG00000139631" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.1.15;4.1.1.29" @@ -147569,7 +147569,7 @@ - MAM02046e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147589,7 +147589,7 @@ - MAM02046e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147609,7 +147609,7 @@ - MAM02963e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147667,7 +147667,7 @@ - MAM02046e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147687,7 +147687,7 @@ - MAM02900e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147707,7 +147707,7 @@ - MAM02901e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147727,7 +147727,7 @@ - MAM02046e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147747,7 +147747,7 @@ - MAM02900e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147767,7 +147767,7 @@ - MAM02901e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147787,7 +147787,7 @@ - MAM02046e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "" @@ -147807,7 +147807,7 @@ - MAM02900e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "" @@ -147827,7 +147827,7 @@ - MAM02901e: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase;Recon3D" - eccodes: "" @@ -147847,7 +147847,7 @@ - MAM02963e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147867,7 +147867,7 @@ - MAM02963e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147887,7 +147887,7 @@ - MAM02963e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -147947,7 +147947,7 @@ - MAM02962e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000021488 or ENSG00000084453 or ENSG00000111700" + - gene_reaction_rule: "ENSG00000084453 or ENSG00000111700" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" From 18782b409eb46424c2b0c6c431de535be92a488b Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 09:00:12 +0800 Subject: [PATCH 15/16] Fix: GPR curation for miscellaneous isolated drug metabolism (#931) * Fix: GPR curation for Miscellaneous_Isolated_Drug_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 42 +++++++++++++++--------------------------- model/genes.tsv | 4 ---- 2 files changed, 15 insertions(+), 31 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 5588d829..a7ca1600 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -161378,7 +161378,7 @@ - MAM02553c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.244" @@ -161486,7 +161486,7 @@ - MAM02470l: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000005381 or ENSG00000115705 or ENSG00000117592 or ENSG00000121053 or ENSG00000167419" + - gene_reaction_rule: "ENSG00000005381 or ENSG00000117592 or ENSG00000121053 or ENSG00000167419" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.11.1.7;1.11.1.8;1.11.2.2" @@ -161523,7 +161523,7 @@ - MAM02040c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000090402 or ENSG00000114982 or ENSG00000168137 or ENSG00000243056 or ENSG00000257335" + - gene_reaction_rule: "ENSG00000090402 or ENSG00000114982 or ENSG00000257335" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.3;3.2.1.10" @@ -161559,7 +161559,7 @@ - MAM02039c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" + - gene_reaction_rule: "ENSG00000167363" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.-" @@ -161578,7 +161578,7 @@ - MAM02039c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" + - gene_reaction_rule: "ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.-" @@ -161908,7 +161908,7 @@ - MAM02527c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111261 or ENSG00000133048 or ENSG00000133063 or ENSG00000134216" + - gene_reaction_rule: "ENSG00000111261 or ENSG00000133063 or ENSG00000134216" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.14" @@ -162075,7 +162075,7 @@ - MAM02128c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000005339 and ENSG00000124151) or ENSG00000083168 or ENSG00000084676 or ENSG00000100393 or ENSG00000103510 or ENSG00000108773 or ENSG00000114166 or ENSG00000125484 or ENSG00000128708 or ENSG00000129873 or ENSG00000134014 or ENSG00000134852 or ENSG00000136504 or ENSG00000156650 or ENSG00000172288 or ENSG00000172352 or ENSG00000172977 or ENSG00000182415 or ENSG00000198408" + - gene_reaction_rule: "(ENSG00000005339 and ENSG00000124151) or ENSG00000083168 or ENSG00000084676 or ENSG00000100393 or ENSG00000103510 or ENSG00000108773 or ENSG00000114166 or ENSG00000125484 or ENSG00000128708 or ENSG00000129873 or ENSG00000134014 or ENSG00000134852 or ENSG00000136504 or ENSG00000156650 or ENSG00000172288 or ENSG00000172352 or ENSG00000172977 or ENSG00000182415" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.48" @@ -162149,7 +162149,7 @@ - MAM02918c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000131238 or ENSG00000221988 or ENSG00000241404" + - gene_reaction_rule: "ENSG00000131238 or ENSG00000241404" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.2.22" @@ -162410,7 +162410,7 @@ - MAM02577c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000153904 or ENSG00000213722" + - gene_reaction_rule: "ENSG00000153904" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.5.3.18" @@ -226820,7 +226820,7 @@ - MAM02555m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.2.1.5" @@ -226860,7 +226860,7 @@ - MAM02555m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.2.1.5" @@ -226900,7 +226900,7 @@ - MAM03136m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.2.1.5" @@ -242378,7 +242378,7 @@ - MAM03164c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000133313 or ENSG00000150656" + - gene_reaction_rule: "ENSG00000133313" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -288366,7 +288366,7 @@ - MAM03418e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000197506" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -288580,7 +288580,7 @@ - MAM03418e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000137860 or ENSG00000156222 or ENSG00000197506" + - gene_reaction_rule: "ENSG00000137860" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -310952,9 +310952,6 @@ - !!omap - id: "ENSG00000168092" - name: "PAFAH1B2" - - !!omap - - id: "ENSG00000168137" - - name: "SETD5" - !!omap - id: "ENSG00000168159" - name: "RNF187" @@ -312593,9 +312590,6 @@ - !!omap - id: "ENSG00000198380" - name: "GFPT1" - - !!omap - - id: "ENSG00000198408" - - name: "OGA" - !!omap - id: "ENSG00000198431" - name: "TXNRD1" @@ -312848,9 +312842,6 @@ - !!omap - id: "ENSG00000213689" - name: "TREX1" - - !!omap - - id: "ENSG00000213722" - - name: "DDAH2" - !!omap - id: "ENSG00000213759" - name: "UGT2B11" @@ -313058,9 +313049,6 @@ - !!omap - id: "ENSG00000242612" - name: "DECR2" - - !!omap - - id: "ENSG00000243056" - - name: "EIF4EBP3" - !!omap - id: "ENSG00000243477" - name: "NAA80" diff --git a/model/genes.tsv b/model/genes.tsv index 70025866..0b40ae59 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2095,7 +2095,6 @@ ENSG00000168003 "ENST00000680729;ENST00000680002;ENST00000377890;ENST00000681467 ENSG00000168032 "ENST00000301825;ENST00000647765;ENST00000439533;ENST00000456402;ENST00000445129" "ENSP00000301825;ENSP00000497683;ENSP00000406555;ENSP00000401565;ENSP00000404671" O75355 ENTPD3 956 ectonucleoside triphosphate diphosphohydrolase 3 "CD39L3;HB6;NTPDase-3" Cell membrane DeepLoc2 ENSG00000168065 "ENST00000377585;ENST00000301891;ENST00000377581;ENST00000490834;ENST00000478051;ENST00000460745;ENST00000428570;ENST00000416590" "ENSP00000366809;ENSP00000301891;ENSP00000366804;ENSP00000394043;ENSP00000413508" Q9NSA0 SLC22A11 55867 solute carrier family 22 member 11 OAT4 Cell membrane DeepLoc2 ENSG00000168092 "ENST00000419197;ENST00000527958;ENST00000304808;ENST00000529887;ENST00000526888;ENST00000530272;ENST00000533206;ENST00000533677" "ENSP00000388742;ENSP00000435289;ENSP00000304006;ENSP00000434951;ENSP00000431365" P68402 PAFAH1B2 5049 platelet activating factor acetylhydrolase 1b catalytic subunit 2 "Nucleus;Cytosol" "SwissProt;CellAtlas" -ENSG00000168137 "ENST00000431285;ENST00000402198;ENST00000683012;ENST00000463180;ENST00000478475;ENST00000415650;ENST00000682536;ENST00000663774;ENST00000683262;ENST00000684606;ENST00000665872;ENST00000666307;ENST00000443339;ENST00000406341;ENST00000670063;ENST00000468208;ENST00000684055;ENST00000407969;ENST00000490791;ENST00000493918;ENST00000399686;ENST00000497213;ENST00000413704;ENST00000466242;ENST00000464410;ENST00000682236;ENST00000488236;ENST00000421188;ENST00000478961;ENST00000476740;ENST00000486465;ENST00000492939;ENST00000459941;ENST00000479538;ENST00000466826" "ENSP00000397076;ENSP00000385852;ENSP00000506933;ENSP00000395959;ENSP00000507956;ENSP00000499452;ENSP00000507464;ENSP00000506817;ENSP00000499600;ENSP00000499402;ENSP00000393221;ENSP00000383939;ENSP00000499725;ENSP00000499609;ENSP00000507953;ENSP00000384114;ENSP00000507055;ENSP00000382593;ENSP00000401554;ENSP00000507801;ENSP00000399993;ENSP00000506929;ENSP00000507322" Q9C0A6 SETD5 55209 SET domain containing 5 FLJ10707 Nucleus "SwissProt;CellAtlas" ENSG00000168159 "ENST00000305943;ENST00000482739" ENSP00000306396 Q5TA31 RNF187 149603 ring finger protein 187 "RACO-1;RACO1" "Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000168237 "ENST00000461183;ENST00000305690;ENST00000473032;ENST00000486393;ENST00000436784;ENST00000471180;ENST00000473583;ENST00000477382;ENST00000489173" "ENSP00000417264;ENSP00000301965;ENSP00000418951;ENSP00000419868;ENSP00000389175;ENSP00000417526;ENSP00000419008" Q8IVS8 GLYCTK 132158 glycerate kinase "HBEBP2;HBEBP4" "Golgi apparatus;Mitochondria;Cytosol" "SwissProt;CellAtlas" ENSG00000168282 ENST00000305386 ENSP00000307423 Q10469 MGAT2 4247 alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase GNT-II Golgi apparatus "SwissProt;CellAtlas" @@ -2634,7 +2633,6 @@ ENSG00000198276 "ENST00000354216;ENST00000369908;ENST00000632800;ENST00000430743 ENSG00000198363 "ENST00000379454;ENST00000541428;ENST00000521909;ENST00000524173;ENST00000521499;ENST00000522349;ENST00000523897;ENST00000523927;ENST00000522919;ENST00000356457;ENST00000519234;ENST00000518068;ENST00000517903;ENST00000517847;ENST00000518441;ENST00000522835;ENST00000519678;ENST00000519264;ENST00000518306;ENST00000520198;ENST00000517856;ENST00000517928;ENST00000389204;ENST00000522603;ENST00000379449;ENST00000517661;ENST00000522325;ENST00000522036;ENST00000522343;ENST00000445642" "ENSP00000368767;ENSP00000437864;ENSP00000479945;ENSP00000429718;ENSP00000478706;ENSP00000430516;ENSP00000348841;ENSP00000427823;ENSP00000429286;ENSP00000430245;ENSP00000429954;ENSP00000429160;ENSP00000483443;ENSP00000479830;ENSP00000427877;ENSP00000429743;ENSP00000373856;ENSP00000436188;ENSP00000368762;ENSP00000428060;ENSP00000394013" Q12797 ASPH 444 aspartate beta-hydroxylase "BAH;CASQ2BP1;HAAH;JCTN" Endoplasmic reticulum "SwissProt;CellAtlas" ENSG00000198373 "ENST00000359154;ENST00000561780;ENST00000569620;ENST00000568845;ENST00000563659;ENST00000569658;ENST00000569174;ENST00000544162;ENST00000567986;ENST00000563618;ENST00000570104;ENST00000569297;ENST00000567579;ENST00000566463;ENST00000568684;ENST00000568185;ENST00000568818;ENST00000567161;ENST00000567303;ENST00000356003" "ENSP00000352069;ENSP00000456451;ENSP00000456582;ENSP00000455347;ENSP00000455311;ENSP00000456216;ENSP00000348283" O00308 WWP2 11060 WW domain containing E3 ubiquitin protein ligase 2 AIP2 Nucleus SwissProt ENSG00000198380 "ENST00000357308;ENST00000361060;ENST00000674507;ENST00000674438;ENST00000494201" "ENSP00000349860;ENSP00000354347;ENSP00000501332;ENSP00000501469;ENSP00000501359" Q06210 GFPT1 2673 glutamine--fructose-6-phosphate transaminase 1 "GFA;GFAT;GFAT1;GFPT" Nucleus CellAtlas -ENSG00000198408 "ENST00000439817;ENST00000361464;ENST00000462994;ENST00000482611;ENST00000357797;ENST00000494347;ENST00000479811;ENST00000461645;ENST00000492204;ENST00000370094;ENST00000429860" "ENSP00000409973;ENSP00000354850;ENSP00000350445;ENSP00000359112;ENSP00000414235" O60502 OGA 10724 O-GlcNAcase "MEA5;MGEA5;NCOAT" "Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000198431 "ENST00000429002;ENST00000525566;ENST00000534282;ENST00000526006;ENST00000526266;ENST00000503506;ENST00000354940;ENST00000388854;ENST00000397736;ENST00000526691;ENST00000531691;ENST00000526390;ENST00000531689;ENST00000529546;ENST00000529751;ENST00000526207;ENST00000528079;ENST00000526580;ENST00000529784;ENST00000524698;ENST00000527688;ENST00000527335;ENST00000526950;ENST00000525265" "ENSP00000412045;ENSP00000434516;ENSP00000431294;ENSP00000421934;ENSP00000347020;ENSP00000373506;ENSP00000380844;ENSP00000435929;ENSP00000431925;ENSP00000435123;ENSP00000433507;ENSP00000434919;ENSP00000432273;ENSP00000433732;ENSP00000433887;ENSP00000436229;ENSP00000433425;ENSP00000433935;ENSP00000433599;ENSP00000432812" Q16881 TXNRD1 7296 thioredoxin reductase 1 "GRIM-12;Trxr1;TXNR" "Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000198488 "ENST00000528622;ENST00000622824" "ENSP00000435628;ENSP00000484640" Q6ZMB0 B3GNT6 192134 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 B3Gn-T6 Golgi apparatus SwissProt ENSG00000198569 "ENST00000673865;ENST00000538474;ENST00000673835;ENST00000673953;ENST00000361134" "ENSP00000501101;ENSP00000442397;ENSP00000501114;ENSP00000501108;ENSP00000355353" Q8N130 SLC34A3 142680 solute carrier family 34 member 3 "FLJ38680;NPTIIc" "Cell membrane;Lysosome" DeepLoc2 @@ -2719,7 +2717,6 @@ ENSG00000213614 "ENST00000268097;ENST00000683243;ENST00000684263;ENST00000683853 ENSG00000213619 "ENST00000533507;ENST00000529276;ENST00000528192;ENST00000530295;ENST00000534208;ENST00000534716;ENST00000263774;ENST00000533105;ENST00000524568;ENST00000677462;ENST00000678975;ENST00000531351;ENST00000525378;ENST00000525212;ENST00000527178" "ENSP00000433753;ENSP00000432099;ENSP00000431588;ENSP00000433405;ENSP00000263774" O75489 NDUFS3 4722 NADH:ubiquinone oxidoreductase core subunit S3 CI-30 "Nucleus;Inner mitochondria" "SwissProt;CellAtlas" ENSG00000213648 "ENST00000360423;ENST00000569544;ENST00000565290;ENST00000563944;ENST00000562941" "ENSP00000353600;ENSP00000455063;ENSP00000456834;ENSP00000457597" P0DMN0 SULT1A4 445329 sulfotransferase family 1A member 4 Cytosol SwissProt ENSG00000213689 "ENST00000433541;ENST00000444177;ENST00000625293;ENST00000492235;ENST00000635452;ENST00000456089" "ENSP00000412404;ENSP00000415972;ENSP00000486676;ENSP00000494511;ENSP00000492023;ENSP00000411331" Q9NSU2 TREX1 11277 three prime repair exonuclease 1 "AGS1;DRN3" "Endoplasmic reticulum;Nucleus;Cytosol" "SwissProt;CellAtlas" -ENSG00000213722 "ENST00000437288;ENST00000436437;ENST00000469963;ENST00000416410;ENST00000480913;ENST00000483792;ENST00000375787;ENST00000375792;ENST00000375789;ENST00000488119" "ENSP00000413164;ENSP00000395759;ENSP00000397466;ENSP00000364943;ENSP00000364949;ENSP00000364945" O95865 DDAH2 23564 dimethylarginine dimethylaminohydrolase 2 G6A "Mitochondria;Cytosol" "SwissProt;CellAtlas" ENSG00000213759 "ENST00000446444;ENST00000513315" ENSP00000387683 O75310 UGT2B11 10720 UDP glucuronosyltransferase family 2 member B11 Endoplasmic reticulum SwissProt ENSG00000213760 "ENST00000376151;ENST00000303892;ENST00000483251;ENST00000415099;ENST00000483170;ENST00000481998" "ENSP00000365321;ENSP00000302194;ENSP00000419698;ENSP00000390148" O95670 ATP6V1G2 534 ATPase H+ transporting V1 subunit G2 "ATP6G;ATP6G2;Em:AC004181.3;NG38;Vma10" Cytosol SwissProt ENSG00000213920 "ENST00000530222;ENST00000396833;ENST00000288087;ENST00000532557;ENST00000531553;ENST00000525696;ENST00000533536;ENST00000532742;ENST00000528849;ENST00000466422" "ENSP00000380045;ENSP00000288087" Q86V88 MDP1 145553 magnesium dependent phosphatase 1 "FN6Pase;MGC5987" Nucleus CellAtlas @@ -2789,7 +2786,6 @@ ENSG00000242110 "ENST00000335606;ENST00000382072;ENST00000506639;ENST00000514195 ENSG00000242366 ENST00000373450 ENSP00000362549 Q9HAW9 UGT1A8 54576 UDP glucuronosyltransferase family 1 member A8 UGT1H Endoplasmic reticulum SwissProt ENSG00000242515 "ENST00000344644;ENST00000373445" "ENSP00000343838;ENSP00000362544" Q9HAW8 UGT1A10 54575 UDP glucuronosyltransferase family 1 member A10 UGT1J Endoplasmic reticulum SwissProt ENSG00000242612 "ENST00000627716;ENST00000424398;ENST00000633923;ENST00000631605;ENST00000219481;ENST00000439661;ENST00000437024;ENST00000633348;ENST00000445291;ENST00000633025;ENST00000461802;ENST00000632744;ENST00000461947;ENST00000465166;ENST00000429116;ENST00000461749;ENST00000469922" "ENSP00000486613;ENSP00000400374;ENSP00000487776;ENSP00000488859;ENSP00000219481;ENSP00000399697;ENSP00000402180;ENSP00000488501;ENSP00000395913;ENSP00000488142;ENSP00000393382" Q9NUI1 DECR2 26063 2,4-dienoyl-CoA reductase 2 "PDCR;SDR17C1" Peroxisome "SwissProt;CellAtlas" -ENSG00000243056 ENST00000310331 ENSP00000308472 O60516 EIF4EBP3 8637 eukaryotic translation initiation factor 4E binding protein 3 4E-BP3 "Cytosol;Nucleus" DeepLoc2 ENSG00000243477 "ENST00000443094;ENST00000354862;ENST00000417393;ENST00000443842;ENST00000450489;ENST00000442620;ENST00000452674" "ENSP00000410610;ENSP00000346927;ENSP00000391893;ENSP00000400559;ENSP00000388316;ENSP00000391158;ENSP00000413623" Q93015 NAA80 24142 N-alpha-acetyltransferase 80, NatH catalytic subunit "FUS2;NAT6" Cytosol SwissProt ENSG00000243480 "ENST00000423678;ENST00000414303;ENST00000497748;ENST00000682202" "ENSP00000390832;ENSP00000397582" P04746 AMY2A 279 amylase alpha 2A AMY2 Extracellular DeepLoc2 ENSG00000243678 "ENST00000514264;ENST00000513177;ENST00000512737;ENST00000503064;ENST00000393183;ENST00000485076;ENST00000393190;ENST00000570801;ENST00000573262" "ENSP00000426976;ENSP00000425581;ENSP00000421064;ENSP00000426901;ENSP00000376880;ENSP00000376886" P22392 NME2 4831 NME/NM23 nucleoside diphosphate kinase 2 "NDPKB;NM23-H2" "Nucleus;Cytosol" "SwissProt;CellAtlas" From 8dda4f78c30cba5466c1452e88e6d0d085a60511 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 09:01:03 +0800 Subject: [PATCH 16/16] Fix: GPR curation for pyrimidine metabolism (#932) * Fix: Pyrimidine_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 31 ++++++++++++++----------------- model/genes.tsv | 1 - 2 files changed, 14 insertions(+), 18 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index a7ca1600..f2c8da17 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -73347,7 +73347,7 @@ - MAM03130c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" + - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.6" @@ -73365,7 +73365,7 @@ - MAM01623c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" + - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.6" @@ -73383,7 +73383,7 @@ - MAM01623m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" + - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.4.6" @@ -73757,7 +73757,7 @@ - MAM03114c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000154269 or ENSG00000183828 or ENSG00000197594" + - gene_reaction_rule: "ENSG00000183828 or ENSG00000197594" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.6.1.8;3.6.1.9;3.6.1.45" @@ -73775,7 +73775,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -73793,7 +73793,7 @@ - MAM02751e: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -73812,7 +73812,7 @@ - MAM02039c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.-" @@ -73911,7 +73911,7 @@ - MAM03130e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125877" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.6.1.19" @@ -73966,7 +73966,7 @@ - MAM02040c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000092964 or ENSG00000147647" + - gene_reaction_rule: "ENSG00000147647" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.5.2.2" @@ -74041,7 +74041,7 @@ - MAM02996m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000185013 or ENSG00000205309" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5;3.1.3.35" @@ -74077,7 +74077,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309" + - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.5" @@ -74277,7 +74277,7 @@ - MAM02759m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000125877 or ENSG00000128951" + - gene_reaction_rule: "ENSG00000128951" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.6.1.23;3.6.1.19" @@ -74332,7 +74332,7 @@ - MAM02039c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000130717 or ENSG00000143179 or ENSG00000198276" + - gene_reaction_rule: "ENSG00000143179 or ENSG00000198276" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.48" @@ -74558,7 +74558,7 @@ - MAM02039c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000167900" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.21" @@ -305801,9 +305801,6 @@ - !!omap - id: "ENSG00000092621" - name: "PHGDH" - - !!omap - - id: "ENSG00000092964" - - name: "DPYSL2" - !!omap - id: "ENSG00000093000" - name: "NUP50" diff --git a/model/genes.tsv b/model/genes.tsv index 0b40ae59..7f93424b 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -390,7 +390,6 @@ ENSG00000092098 "ENST00000560875;ENST00000559308;ENST00000558634;ENST00000557878 ENSG00000092148 "ENST00000554882;ENST00000399332;ENST00000555843;ENST00000611816;ENST00000553700;ENST00000556281;ENST00000557695;ENST00000555311;ENST00000553957;ENST00000557321;ENST00000554027;ENST00000555915;ENST00000556004;ENST00000557369;ENST00000554850;ENST00000556224;ENST00000554471;ENST00000553616;ENST00000556474" "ENSP00000451260;ENSP00000382269;ENSP00000484981;ENSP00000450697;ENSP00000451860;ENSP00000450920;ENSP00000452233;ENSP00000452015;ENSP00000479695" Q9ULT8 HECTD1 25831 HECT domain E3 ubiquitin protein ligase 1 KIAA1131 Nucleus CellAtlas ENSG00000092295 "ENST00000206765;ENST00000544573;ENST00000559669;ENST00000559136;ENST00000558074;ENST00000560443;ENST00000560478;ENST00000560226;ENST00000561067" "ENSP00000206765;ENSP00000439446;ENSP00000453701;ENSP00000453337;ENSP00000453840;ENSP00000452822;ENSP00000453234;ENSP00000454070;ENSP00000452690" P22735 TGM1 7051 transglutaminase 1 "ICR2;LI;LI1;TGASE;TGK" Cytosol DeepLoc2 ENSG00000092621 "ENST00000641597;ENST00000493622;ENST00000641720;ENST00000642041;ENST00000641947;ENST00000641213;ENST00000641074;ENST00000496756;ENST00000641115;ENST00000642021;ENST00000641491;ENST00000369409;ENST00000641023;ENST00000641513;ENST00000641573;ENST00000641587;ENST00000641570;ENST00000641891;ENST00000641375;ENST00000462324;ENST00000641371;ENST00000641272;ENST00000641247;ENST00000641756;ENST00000641711;ENST00000641927;ENST00000641314;ENST00000369407;ENST00000641811;ENST00000641847;ENST00000641455;ENST00000469443;ENST00000641939;ENST00000482968" "ENSP00000493382;ENSP00000493433;ENSP00000492948;ENSP00000493415;ENSP00000492994;ENSP00000493079;ENSP00000493446;ENSP00000493264;ENSP00000493187;ENSP00000358417;ENSP00000493175;ENSP00000493398;ENSP00000493453;ENSP00000493213;ENSP00000493288;ENSP00000493089;ENSP00000493305;ENSP00000493432;ENSP00000492955;ENSP00000493147;ENSP00000493296" O43175 PHGDH 26227 phosphoglycerate dehydrogenase "PDG;PGDH;SERA" "Cytosol;Nucleus" CellAtlas -ENSG00000092964 "ENST00000521913;ENST00000493789;ENST00000311151;ENST00000523027;ENST00000523690;ENST00000523093;ENST00000521983;ENST00000474808" "ENSP00000427985;ENSP00000427954;ENSP00000309539;ENSP00000431117" Q16555 DPYSL2 1808 dihydropyrimidinase like 2 "CRMP2;DHPRP2;DRP-2;DRP2" Cytosol "SwissProt;CellAtlas" ENSG00000093000 "ENST00000347635;ENST00000407019;ENST00000424634;ENST00000417702;ENST00000497960;ENST00000461437;ENST00000434760;ENST00000430547;ENST00000484186;ENST00000445721;ENST00000493456;ENST00000396096;ENST00000461194;ENST00000432340;ENST00000419387;ENST00000422489;ENST00000486184;ENST00000491860;ENST00000469163" "ENSP00000345895;ENSP00000385555;ENSP00000415062;ENSP00000394450;ENSP00000388426;ENSP00000397960;ENSP00000398297;ENSP00000379403;ENSP00000400465;ENSP00000391987;ENSP00000416264" Q9UKX7 NUP50 10762 nucleoporin 50 NPAP60L Nucleus "SwissProt;CellAtlas" ENSG00000093010 "ENST00000676678;ENST00000403184;ENST00000361682;ENST00000403710;ENST00000407537;ENST00000467943;ENST00000678868;ENST00000678769;ENST00000428707;ENST00000412786;ENST00000207636;ENST00000406520;ENST00000678255;ENST00000449653;ENST00000677397;ENST00000678240;ENST00000677675;ENST00000493893;ENST00000678945;ENST00000677564;ENST00000677470" "ENSP00000503719;ENSP00000383966;ENSP00000354511;ENSP00000385917;ENSP00000384654;ENSP00000503583;ENSP00000503289;ENSP00000387695;ENSP00000403958;ENSP00000207636;ENSP00000385150;ENSP00000504402;ENSP00000416778;ENSP00000503422" P21964 COMT 1312 catechol-O-methyltransferase "Endoplasmic reticulum;Cytosol" "SwissProt;CellAtlas" ENSG00000093072 "ENST00000399837;ENST00000399839;ENST00000330232;ENST00000262607;ENST00000648668;ENST00000648061;ENST00000449907;ENST00000649540;ENST00000649915;ENST00000469063;ENST00000480276;ENST00000650635;ENST00000648343;ENST00000543038;ENST00000441548;ENST00000649310;ENST00000649746;ENST00000610390" "ENSP00000382731;ENSP00000382733;ENSP00000332871;ENSP00000262607;ENSP00000496894;ENSP00000406443;ENSP00000497469;ENSP00000497681;ENSP00000442482;ENSP00000392078;ENSP00000496839;ENSP00000497913;ENSP00000483418" Q9NZK5 ADA2 51816 adenosine deaminase 2 "ADGF;CECR1;IDGFL" Lysosome DeepLoc2