From 84b3cbd1ea1d769923fb7fe8c4dd544a7ded134e Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Fri, 14 Apr 2023 14:14:39 +0200 Subject: [PATCH 1/7] fix: update GPRs for Cytochrome C Oxidoreductase, as proposed in #526 --- model/Human-GEM.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 393fc2cf..9eb3d4b0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -94384,7 +94384,7 @@ - MAM02630m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111775 and ENSG00000112695 and ENSG00000126267 and ENSG00000127184 and ENSG00000131143 and ENSG00000131174 and ENSG00000135940 and ENSG00000164919 and ENSG00000176340 and ENSG00000178741 and ENSG00000198712 and ENSG00000198804 and ENSG00000198938 and ENSG00000189043" + - gene_reaction_rule: "ENSG00000198804 and ENSG00000198712 and ENSG00000198938 and (ENSG00000131143 or ENSG00000131055) and ENSG00000178741 and ENSG00000135940 and (ENSG00000111775 or ENSG00000156885) and (ENSG00000126267 or ENSG00000160471) and ENSG00000164919 and (ENSG00000161281 or ENSG00000112695) and ENSG00000131174 and ENSG00000170516 and ENSG00000127184 and ENSG00000176340 and ENSG00000189043" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.9.3.1" @@ -302290,7 +302290,7 @@ - MAM02631m: 0.02 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111775 and ENSG00000112695 and ENSG00000126267 and ENSG00000127184 and ENSG00000131055 and ENSG00000131143 and ENSG00000131174 and ENSG00000135940 and ENSG00000156885 and ENSG00000160471 and ENSG00000161281 and ENSG00000164919 and ENSG00000170516 and ENSG00000176340 and ENSG00000178741 and ENSG00000187581 and ENSG00000198712 and ENSG00000198804 and ENSG00000198938" + - gene_reaction_rule: "ENSG00000198804 and ENSG00000198712 and ENSG00000198938 and (ENSG00000131143 or ENSG00000131055) and ENSG00000178741 and ENSG00000135940 and (ENSG00000111775 or ENSG00000156885) and (ENSG00000126267 or ENSG00000160471) and ENSG00000164919 and (ENSG00000161281 or ENSG00000112695) and ENSG00000131174 and ENSG00000170516 and ENSG00000127184 and ENSG00000176340 and ENSG00000189043" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" From 8e4f2d255ff130b5bc0b538bef5a8a480217a975 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Fri, 14 Apr 2023 17:06:16 +0200 Subject: [PATCH 2/7] fix: remove MAR04456 that's duplicate to MAR04458+MAR04589 --- model/Human-GEM.yml | 16 ---------------- model/reactions.tsv | 1 - 2 files changed, 17 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 9eb3d4b0..078b71ed 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -93858,22 +93858,6 @@ - subsystem: - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism" - confidence_score: 0 - - !!omap - - id: "MAR04456" - - name: "citrate hydroxymutase" - - metabolites: !!omap - - MAM01587m: -1 - - MAM02183m: 1 - - lower_bound: -1000 - - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100412 or ENSG00000122729" - - rxnNotes: "" - - rxnFrom: "HMRdatabase" - - eccodes: "4.2.1.3" - - references: "PMID:15263083;PMID:16511074" - - subsystem: - - "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism" - - confidence_score: 0 - !!omap - id: "MAR04458" - name: "citrate hydro-lyase (cis-aconitate-forming)" diff --git a/model/reactions.tsv b/model/reactions.tsv index 76dd1e1e..d845cd99 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -1347,7 +1347,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04408" "R01082" "FUM" "R01082C" "r0258" "" "FUM" "MNXR99705" "HMR_4408" "RCR10105" "" 0 "" "RHEA:12460" "HMR_4408" "MAR04410" "R01082" "FUMm" "R01082C" "r0259" "" "FUMm" "MNXR99705" "HMR_4410" "RCR11665" "" 0 "" "RHEA:12460" "HMR_4410" "MAR04454" "R01324" "ACONT" "R01324C" "r0315" "" "ACONT" "MNXR95384" "HMR_4454" "RCR10028" "" 0 "" "RHEA:10336" "HMR_4454" -"MAR04456" "R01324" "ACONTm" "R01324C" "r0316" "" "ACONTm" "MNXR95384" "HMR_4456" "RCR10351" "" 0 "" "RHEA:10336" "HMR_4456" "MAR04458" "R01325" "" "R01325C" "r0317" "" "r0317" "MNXR105321;MNXR95386" "HMR_4458" "RCR10106" "" 0 "RHEA:10231" "RHEA:10228" "HMR_4458" "MAR04465" "R01392" "HPYRRy" "R01392C" "r0327" "" "HPYRRy" "MNXR100336" "HMR_4465" "RCR11666" "" 0 "" "RHEA:18657" "HMR_4465" "MAR04589" "R01900" "" "R01900C" "r0426" "" "r0426" "MNXR105342;MNXR95387" "HMR_4589" "RCR10352" "" 0 "" "RHEA:22144" "HMR_4589" From c94e0c6281a52b8e29e9386820f12212db6e9df3 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Fri, 14 Apr 2023 17:11:51 +0200 Subject: [PATCH 3/7] data: sync deleted rxn to deprecatedReactions.tsv --- data/deprecatedIdentifiers/deprecatedReactions.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index 00f0b54f..f72550cf 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -70,3 +70,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx "MAR04586" "R01899" "" "R01899C" "r0423" "" "r0423" "MNXR105340" "HMR_4586" "RCR11668" "" 0 "" "RHEA:25588" "HMR_4586" "MAR04587" "R01899" "" "R01899C" "r0424" "" "r0424" "MNXR105340" "HMR_4587" "RCR10604" "" 0 "" "RHEA:25588" "HMR_4587" "MAR04588" "" "" "" "r0425" "" "r0425" "MNXR105341" "HMR_4588" "RCR11669" "" 0 "" "" "HMR_4588" +"MAR04456" "R01324" "ACONTm" "R01324C" "r0316" "" "ACONTm" "MNXR95384" "HMR_4456" "RCR10351" "" 0 "" "RHEA:10336" "HMR_4456" From 62a9e8929f7696115537727fc4841fadf4ab1d38 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Fri, 14 Apr 2023 21:44:37 +0200 Subject: [PATCH 4/7] fix: assign comp-specific GPR to MAR04454, MAR04458, MAR04589 --- model/Human-GEM.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 078b71ed..e8671a01 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -93850,7 +93850,7 @@ - MAM02183c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000122729 or ENSG00000136381" + - gene_reaction_rule: "ENSG00000122729" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.3" @@ -93867,7 +93867,7 @@ - MAM02040m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100412 or ENSG00000122729" + - gene_reaction_rule: "ENSG00000100412" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.3" @@ -93903,7 +93903,7 @@ - MAM02183m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100412 or ENSG00000122729" + - gene_reaction_rule: "ENSG00000100412" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.3" From f8f6706e25c5b02aa7773aef876e4f36ea9d0cdc Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Fri, 14 Apr 2023 22:16:46 +0200 Subject: [PATCH 5/7] fix-gene: remove ENSG00000136381 from MAR04454 --- model/Human-GEM.yml | 2 -- model/genes.tsv | 1 - 2 files changed, 3 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e8671a01..b341d81a 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -307399,8 +307399,6 @@ - id: "ENSG00000136267" - !!omap - id: "ENSG00000136371" - - !!omap - - id: "ENSG00000136381" - !!omap - id: "ENSG00000136448" - !!omap diff --git a/model/genes.tsv b/model/genes.tsv index fd2bf656..0f23bf9c 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -1302,7 +1302,6 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000136250" "ENST00000617537;ENST00000621510;ENST00000617267;ENST00000614254;ENST00000491444;ENST00000487014;ENST00000495942;ENST00000480201;ENST00000543742;ENST00000435386;ENST00000414637;ENST00000612871" "ENSP00000483783;ENSP00000479664;ENSP00000416051;ENSP00000416472;ENSP00000484305" "P28039" "AOAH" "313" "acyloxyacyl hydrolase" "" "Cytosol" "SwissProt" "ENSG00000136267" "ENST00000403951;ENST00000402815;ENST00000407950;ENST00000493142;ENST00000406247;ENST00000403963;ENST00000471732;ENST00000477401;ENST00000464065;ENST00000467449;ENST00000437998;ENST00000463981;ENST00000399322" "ENSP00000385780;ENSP00000384909;ENSP00000385031;ENSP00000386066;ENSP00000405569;ENSP00000382260" "Q9Y6T7" "DGKB" "1607" "diacylglycerol kinase beta" "DAGK2;DGK;DGK-BETA;KIAA0718" "Cytosol" "SwissProt" "ENSG00000136371" "ENST00000560261;ENST00000258874;ENST00000559722;ENST00000560919" "ENSP00000454318;ENSP00000258874;ENSP00000489076;ENSP00000454626" "P49914" "MTHFS" "10588" "methenyltetrahydrofolate synthetase" "HsT19268" "Cytosol" "SwissProt;CellAtlas" -"ENSG00000136381" "ENST00000560840;ENST00000559215;ENST00000258886;ENST00000558525;ENST00000560440;ENST00000558570;ENST00000560454;ENST00000559427;ENST00000559676;ENST00000559091" "ENSP00000453172;ENSP00000453532;ENSP00000258886;ENSP00000453058;ENSP00000452938;ENSP00000454063;ENSP00000453863" "P48200" "IREB2" "3658" "iron responsive element binding protein 2" "IRP2" "Cytosol" "SwissProt;CellAtlas" "ENSG00000136448" "ENST00000678938;ENST00000592782;ENST00000676828;ENST00000590310;ENST00000677949;ENST00000591931;ENST00000678606;ENST00000587014;ENST00000587670;ENST00000258960;ENST00000678576;ENST00000543908;ENST00000676753;ENST00000678332;ENST00000590114;ENST00000585561;ENST00000592654;ENST00000588455;ENST00000587120" "ENSP00000503621;ENSP00000468424;ENSP00000504192;ENSP00000503657;ENSP00000504048;ENSP00000504365;ENSP00000258960;ENSP00000503635;ENSP00000439263;ENSP00000503505;ENSP00000504484;ENSP00000504284;ENSP00000466777;ENSP00000466827" "P30419" "NMT1" "4836" "N-myristoyltransferase 1" "NMT" "Cytosol" "SwissProt;CellAtlas" "ENSG00000136504" "ENST00000675278;ENST00000454930;ENST00000259021;ENST00000509773;ENST00000510819;ENST00000424009;ENST00000509124;ENST00000506533;ENST00000435742;ENST00000513171;ENST00000514540;ENST00000513980;ENST00000512616;ENST00000508594;ENST00000509794;ENST00000510426;ENST00000513075;ENST00000503101;ENST00000503635" "ENSP00000502732;ENSP00000413415;ENSP00000259021;ENSP00000424577;ENSP00000423385;ENSP00000398961;ENSP00000421368;ENSP00000409477" "O95251" "KAT7" "11143" "lysine acetyltransferase 7" "HBO1;HBOA;MYST2;ZC2HC7" "Nucleus;Cytosol" "SwissProt;CellAtlas" "ENSG00000136521" "ENST00000488002;ENST00000611971;ENST00000493866;ENST00000259037;ENST00000472629;ENST00000468210;ENST00000359944;ENST00000477177;ENST00000482604;ENST00000480374;ENST00000496904;ENST00000473500;ENST00000491054;ENST00000471112;ENST00000476587;ENST00000493716" "ENSP00000481703;ENSP00000419656;ENSP00000259037;ENSP00000419248;ENSP00000420538;ENSP00000353026;ENSP00000418354;ENSP00000419099;ENSP00000419501" "O43674" "NDUFB5" "4711" "NADH:ubiquinone oxidoreductase subunit B5" "CI-SGDH;MGC12314;SGDH" "Nucleus;Inner mitochondria" "SwissProt;CellAtlas" From d73f951cc0f8921b1e182604aeb752f8cd7942b9 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sun, 16 Apr 2023 19:13:39 +0200 Subject: [PATCH 6/7] fix-rxn: block MAR13081 ub=lb=0 - avoid ROX version complex IV from carrying flux - remove COX8C (ENSG00000187581) --- model/Human-GEM.yml | 4 +--- model/genes.tsv | 1 - 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index b341d81a..3bfff112 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -302273,7 +302273,7 @@ - MAM02630m: -1 - MAM02631m: 0.02 - lower_bound: 0 - - upper_bound: 1000 + - upper_bound: 0 - gene_reaction_rule: "ENSG00000198804 and ENSG00000198712 and ENSG00000198938 and (ENSG00000131143 or ENSG00000131055) and ENSG00000178741 and ENSG00000135940 and (ENSG00000111775 or ENSG00000156885) and (ENSG00000126267 or ENSG00000160471) and ENSG00000164919 and (ENSG00000161281 or ENSG00000112695) and ENSG00000131174 and ENSG00000170516 and ENSG00000127184 and ENSG00000176340 and ENSG00000189043" - rxnNotes: "" - rxnFrom: "Recon3D" @@ -309933,8 +309933,6 @@ - id: "ENSG00000187555" - !!omap - id: "ENSG00000187566" - - !!omap - - id: "ENSG00000187581" - !!omap - id: "ENSG00000187630" - !!omap diff --git a/model/genes.tsv b/model/genes.tsv index 0f23bf9c..fbc9b739 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2569,7 +2569,6 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000187531" "ENST00000574992;ENST00000572976;ENST00000571832;ENST00000328666;ENST00000536038;ENST00000574153;ENST00000576156;ENST00000571233;ENST00000572902;ENST00000572350;ENST00000577065;ENST00000574495;ENST00000573367;ENST00000571915;ENST00000575360;ENST00000575244;ENST00000570367;ENST00000572671;ENST00000571213;ENST00000573576;ENST00000574915" "ENSP00000329466;ENSP00000461044;ENSP00000459524" "Q9NRC8" "SIRT7" "51547" "sirtuin 7" "" "Nucleus;Cytosol" "SwissProt;CellAtlas" "ENSG00000187555" "ENST00000344836;ENST00000673704;ENST00000563961;ENST00000381886;ENST00000565455;ENST00000563085;ENST00000567113;ENST00000565883;ENST00000562615;ENST00000563043;ENST00000562051;ENST00000567692;ENST00000569448;ENST00000566131;ENST00000570256;ENST00000567329;ENST00000542333;ENST00000566004;ENST00000569230;ENST00000566273;ENST00000564117;ENST00000566224" "ENSP00000343535;ENSP00000501290;ENSP00000454362;ENSP00000371310;ENSP00000456258;ENSP00000454795;ENSP00000459594;ENSP00000458027;ENSP00000439272;ENSP00000456150;ENSP00000457237;ENSP00000455719;ENSP00000457815" "Q93009" "USP7" "7874" "ubiquitin specific peptidase 7" "HAUSP" "Nucleus;Cytosol" "SwissProt;CellAtlas" "ENSG00000187566" "ENST00000340650" "ENSP00000345464" "Q6VVB1" "NHLRC1" "378884" "NHL repeat containing E3 ubiquitin protein ligase 1" "bA204B7.2;EPM2B" "Endoplasmic reticulum;Nucleus" "SwissProt" -"ENSG00000187581" "ENST00000342144" "ENSP00000340568" "Q7Z4L0" "COX8C" "341947" "cytochrome c oxidase subunit 8C" "COX8-3" "Mitochondria" "DeepLoc2" "ENSG00000187630" "ENST00000534993;ENST00000543805;ENST00000621761;ENST00000397071;ENST00000559411;ENST00000558753;ENST00000537912;ENST00000335125;ENST00000559387;ENST00000557812;ENST00000560276" "ENSP00000441095;ENSP00000441433;ENSP00000481066;ENSP00000380261;ENSP00000453889;ENSP00000453845;ENSP00000439942;ENSP00000334801;ENSP00000453173;ENSP00000452875" "Q6PKH6" "DHRS4L2" "317749" "dehydrogenase/reductase 4 like 2" "SDR25C3" "Nucleus" "CellAtlas" "ENSG00000187676" "ENST00000343307;ENST00000461652" "ENSP00000343002" "Q6Y288" "B3GLCT" "145173" "beta 3-glucosyltransferase" "B3GALTL;B3Glc-T;B3GTL" "Endoplasmic reticulum" "SwissProt" "ENSG00000187714" "ENST00000374115" "ENSP00000363229" "Q16572" "SLC18A3" "6572" "solute carrier family 18 member A3" "VACHT" "Cell membrane;Lysosome" "DeepLoc2" From e9b0f73d53eccde8aeee9cb806b515a59a080263 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Tue, 18 Apr 2023 08:21:35 +0200 Subject: [PATCH 7/7] doc: log the purpose and blocking of MAR13081 --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 3bfff112..d94ac61b 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -302275,7 +302275,7 @@ - lower_bound: 0 - upper_bound: 0 - gene_reaction_rule: "ENSG00000198804 and ENSG00000198712 and ENSG00000198938 and (ENSG00000131143 or ENSG00000131055) and ENSG00000178741 and ENSG00000135940 and (ENSG00000111775 or ENSG00000156885) and (ENSG00000126267 or ENSG00000160471) and ENSG00000164919 and (ENSG00000161281 or ENSG00000112695) and ENSG00000131174 and ENSG00000170516 and ENSG00000127184 and ENSG00000176340 and ENSG00000189043" - - rxnNotes: "" + - rxnNotes: "This is ROS version of Complex IV, and blocked by default" - rxnFrom: "Recon3D" - eccodes: "" - references: ""