From f299b9afeed50eb661349a83d04d0d21767ba307 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Tue, 24 Jan 2023 21:56:05 +0100 Subject: [PATCH 1/4] fix-gene: add subunit NDUFA7 (ENSG00000267855) to Complex I --- model/Human-GEM.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 41f41845..a98ea618 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -4,7 +4,7 @@ short_name: "Human-GEM" full_name: "Generic genome-scale metabolic model of Homo sapiens" version: "" - date: "2023-01-23" + date: "2023-01-24" authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas" email: "jonrob@chalmers.se" organization: "Chalmers University of Technology" @@ -94628,7 +94628,7 @@ - MAM03103m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000004779 and ENSG00000023228 and ENSG00000065518 and ENSG00000090266 and ENSG00000099795 and ENSG00000109390 and ENSG00000110717 and ENSG00000115286 and ENSG00000119013 and ENSG00000119421 and ENSG00000125356 and ENSG00000128609 and ENSG00000130414 and ENSG00000131495 and ENSG00000136521 and ENSG00000139180 and ENSG00000140990 and ENSG00000145494 and ENSG00000147123 and ENSG00000147684 and ENSG00000151366 and ENSG00000158864 and ENSG00000160194 and ENSG00000164258 and ENSG00000165264 and ENSG00000166136 and ENSG00000167792 and ENSG00000168653 and ENSG00000170906 and ENSG00000174886 and ENSG00000178127 and ENSG00000183648 and ENSG00000184752 and ENSG00000184983 and ENSG00000186010 and ENSG00000189043 and ENSG00000198695 and ENSG00000198763 and ENSG00000198786 and ENSG00000198840 and ENSG00000198886 and ENSG00000198888 and ENSG00000212907 and ENSG00000213619" + - gene_reaction_rule: "ENSG00000004779 and ENSG00000023228 and ENSG00000065518 and ENSG00000090266 and ENSG00000099795 and ENSG00000109390 and ENSG00000110717 and ENSG00000115286 and ENSG00000119013 and ENSG00000119421 and ENSG00000125356 and ENSG00000128609 and ENSG00000130414 and ENSG00000131495 and ENSG00000136521 and ENSG00000139180 and ENSG00000140990 and ENSG00000145494 and ENSG00000147123 and ENSG00000147684 and ENSG00000151366 and ENSG00000158864 and ENSG00000160194 and ENSG00000164258 and ENSG00000165264 and ENSG00000166136 and ENSG00000167792 and ENSG00000168653 and ENSG00000170906 and ENSG00000174886 and ENSG00000178127 and ENSG00000183648 and ENSG00000184752 and ENSG00000184983 and ENSG00000186010 and ENSG00000189043 and ENSG00000198695 and ENSG00000198763 and ENSG00000198786 and ENSG00000198840 and ENSG00000198886 and ENSG00000198888 and ENSG00000212907 and ENSG00000213619 and ENSG00000267855" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.6.5.3" @@ -306137,6 +306137,8 @@ - id: "ENSG00000102743" - !!omap - id: "ENSG00000102780" + - !!omap + - id: "ENSG00000102794" - !!omap - id: "ENSG00000102858" - !!omap @@ -311027,6 +311029,8 @@ - id: "ENSG00000265491" - !!omap - id: "ENSG00000266200" + - !!omap + - id: "ENSG00000267855" - !!omap - id: "ENSG00000268104" - !!omap @@ -311079,8 +311083,6 @@ - id: "ENSG00000288702" - !!omap - id: "ENSG00000288705" - - !!omap - - id: "ENSG00000102794" - compartments: !!omap - e: "Extracellular" - x: "Peroxisome" From 9cdd5b5bdb8c504f2f7cab53c249637a420c3ddb Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Tue, 24 Jan 2023 22:16:19 +0100 Subject: [PATCH 2/4] fix-gene: update genes.tsv --- model/genes.tsv | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/model/genes.tsv b/model/genes.tsv index 5e41fc69..23c63d5d 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -552,6 +552,7 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000102699" "ENST00000381989;ENST00000484989;ENST00000480576" "ENSP00000371419" "Q9UKK3" "PARP4" "143" "poly(ADP-ribose) polymerase family member 4" "ADPRTL1;ARTD4;p193;VAULT3;VPARP;VWA5C" "Nucleus;Cytosol" "SwissProt;CellAtlas" "ENSG00000102743" "ENST00000478827;ENST00000338625;ENST00000417731;ENST00000470509" "ENSP00000342267;ENSP00000415826;ENSP00000431429" "Q9Y619" "SLC25A15" "10166" "solute carrier family 25 member 15" "D13S327;HHH;ORC1;ORNT1" "Inner mitochondria" "SwissProt" "ENSG00000102780" "ENST00000337343;ENST00000261491;ENST00000611224;ENST00000628433;ENST00000627777;ENST00000626247;ENST00000536612;ENST00000498255;ENST00000489851;ENST00000379274" "ENSP00000337572;ENSP00000261491;ENSP00000482250;ENSP00000485809;ENSP00000486838;ENSP00000486329;ENSP00000445114;ENSP00000368576" "Q86XP1" "DGKH" "160851" "diacylglycerol kinase eta" "DGKeta" "Cytosol" "SwissProt" +"ENSG00000102794" "ENST00000377462;ENST00000449753" "ENSP00000366682;ENSP00000401584" "A6NK06" "ACOD1" "730249" "aconitate decarboxylase 1" "CAD;IRG1" "Mitochondria" "SwissProt" "ENSG00000102858" "ENST00000591895;ENST00000262370;ENST00000536343;ENST00000587747;ENST00000399577;ENST00000588994;ENST00000586183;ENST00000615397;ENST00000590790;ENST00000593224;ENST00000587145;ENST00000590457;ENST00000588015;ENST00000591673;ENST00000592256;ENST00000588111;ENST00000585676;ENST00000415496" "ENSP00000468171;ENSP00000262370;ENSP00000443810;ENSP00000467414;ENSP00000382487;ENSP00000468819;ENSP00000465860;ENSP00000464811;ENSP00000465249;ENSP00000393311" "O60291" "MGRN1" "23295" "mahogunin ring finger 1" "KIAA0544;RNF156" "Endoplasmic reticulum;Nucleus;Cytosol" "SwissProt;CellAtlas" "ENSG00000102893" "ENST00000566037;ENST00000566044;ENST00000299167;ENST00000323584;ENST00000566721;ENST00000565424;ENST00000567402;ENST00000563376;ENST00000567200;ENST00000564873;ENST00000570047;ENST00000566436;ENST00000568439;ENST00000568171;ENST00000566275;ENST00000566319;ENST00000564711" "ENSP00000455664;ENSP00000456729;ENSP00000299167;ENSP00000313504;ENSP00000457905;ENSP00000458581;ENSP00000460408;ENSP00000461770;ENSP00000458446;ENSP00000459287;ENSP00000458961" "Q93100" "PHKB" "5257" "phosphorylase kinase regulatory subunit beta" "" "Golgi apparatus;Cytosol" "SwissProt;CellAtlas" "ENSG00000102900" "ENST00000308159;ENST00000563858;ENST00000566315;ENST00000569842;ENST00000569863;ENST00000562496;ENST00000568656;ENST00000566678;ENST00000564887;ENST00000569595;ENST00000566727;ENST00000567641;ENST00000568283;ENST00000567081;ENST00000542526;ENST00000563437;ENST00000563405;ENST00000563486;ENST00000569322;ENST00000564278;ENST00000563465" "ENSP00000310668;ENSP00000455230;ENSP00000456264;ENSP00000458101;ENSP00000454587;ENSP00000457902;ENSP00000454285;ENSP00000454935;ENSP00000458039;ENSP00000455210;ENSP00000454844;ENSP00000455181;ENSP00000440235;ENSP00000458078;ENSP00000456196;ENSP00000457907" "Q8N1F7" "NUP93" "9688" "nucleoporin 93" "KIAA0095" "Nucleus" "SwissProt" @@ -2997,6 +2998,7 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000265203" "ENST00000584701" "ENSP00000463151" "P10745" "RBP3" "5949" "retinol binding protein 3" "D10S64;D10S65;D10S66;RP66" "Extracellular" "DeepLoc2" "ENSG00000265491" "ENST00000582693;ENST00000539368" "ENSP00000463650" "Q9Y4L5" "RNF115" "27246" "ring finger protein 115" "CL469780;ZNF364" "Mitochondria;Nucleus;Cytosol;Lysosome" "SwissProt;CellAtlas" "ENSG00000266200" "ENST00000579578;ENST00000586762;ENST00000588823;ENST00000611850;ENST00000591655" "ENSP00000463502;ENSP00000480815;ENSP00000468117" "P54317" "PNLIPRP2" "5408" "pancreatic lipase related protein 2 (gene/pseudogene)" "PLRP2" "Extracellular" "DeepLoc2" +"ENSG00000267855" "ENST00000301457;ENST00000593729;ENST00000595856;ENST00000601101;ENST00000601258;ENST00000602059" "ENSP00000301457" "O95182" "NDUFA7" "4701" "NADH:ubiquinone oxidoreductase subunit A7" "CAD;IRG1" "Inner mitochondria" "SwissProt" "ENSG00000268104" "ENST00000598581;ENST00000463626" "ENSP00000470801" "Q9UN76" "SLC6A14" "11254" "solute carrier family 6 member 14" "" "Cell membrane" "DeepLoc2" "ENSG00000268606" "ENST00000620710;ENST00000595583;ENST00000617846;ENST00000617505;ENST00000623806;ENST00000623438;ENST00000611557;ENST00000598543;ENST00000611674;ENST00000684311" "ENSP00000484290;ENSP00000470872;ENSP00000482879;ENSP00000483352;ENSP00000485541;ENSP00000485391;ENSP00000480738;ENSP00000469919;ENSP00000480491;ENSP00000507899" "P43356" "MAGEA2" "4101" "MAGE family member A2" "CT1.2;MAGE2;MAGEA2A" "Nucleus" "SwissProt" "ENSG00000271567" "ENST00000581164" "ENSP00000463419" "A0A075B759" "PPIAL4E" "730262" "peptidylprolyl isomerase A like 4E" "" "Cytosol" "DeepLoc2" @@ -3023,4 +3025,3 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000285269" "ENST00000464104;ENST00000463517;ENST00000643789" "ENSP00000494818" "" "" "11046" "novel transcript, SLC35D2-HSD17B3 readthrough" "" "Endoplasmic reticulum;Golgi apparatus" "DeepLoc2" "ENSG00000288702" "ENST00000482026" "ENSP00000418532" "P35503" "UGT1A3" "54659" "UDP glucuronosyltransferase family 1 member A3" "UGT1C" "Endoplasmic reticulum" "SwissProt" "ENSG00000288705" "ENST00000373414" "ENSP00000362513" "P35504" "UGT1A5" "54579" "UDP glucuronosyltransferase family 1 member A5" "UGT1E" "Endoplasmic reticulum" "SwissProt" -"ENSG00000102794" "ENST00000377462;ENST00000449753" "ENSP00000366682;ENSP00000401584" "A6NK06" "ACOD1" "730249" "aconitate decarboxylase 1" "CAD;IRG1" "Mitochondria" "SwissProt" From 6eb3ce946d0db1cdaa0a34810b600394dc87e16e Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Wed, 25 Jan 2023 14:30:54 +0100 Subject: [PATCH 3/4] fix-gene: remove incorrect synonyms --- model/genes.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/genes.tsv b/model/genes.tsv index 23c63d5d..9f6bc822 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2998,7 +2998,7 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000265203" "ENST00000584701" "ENSP00000463151" "P10745" "RBP3" "5949" "retinol binding protein 3" "D10S64;D10S65;D10S66;RP66" "Extracellular" "DeepLoc2" "ENSG00000265491" "ENST00000582693;ENST00000539368" "ENSP00000463650" "Q9Y4L5" "RNF115" "27246" "ring finger protein 115" "CL469780;ZNF364" "Mitochondria;Nucleus;Cytosol;Lysosome" "SwissProt;CellAtlas" "ENSG00000266200" "ENST00000579578;ENST00000586762;ENST00000588823;ENST00000611850;ENST00000591655" "ENSP00000463502;ENSP00000480815;ENSP00000468117" "P54317" "PNLIPRP2" "5408" "pancreatic lipase related protein 2 (gene/pseudogene)" "PLRP2" "Extracellular" "DeepLoc2" -"ENSG00000267855" "ENST00000301457;ENST00000593729;ENST00000595856;ENST00000601101;ENST00000601258;ENST00000602059" "ENSP00000301457" "O95182" "NDUFA7" "4701" "NADH:ubiquinone oxidoreductase subunit A7" "CAD;IRG1" "Inner mitochondria" "SwissProt" +"ENSG00000267855" "ENST00000301457;ENST00000593729;ENST00000595856;ENST00000601101;ENST00000601258;ENST00000602059" "ENSP00000301457" "O95182" "NDUFA7" "4701" "NADH:ubiquinone oxidoreductase subunit A7" "" "Inner mitochondria" "SwissProt" "ENSG00000268104" "ENST00000598581;ENST00000463626" "ENSP00000470801" "Q9UN76" "SLC6A14" "11254" "solute carrier family 6 member 14" "" "Cell membrane" "DeepLoc2" "ENSG00000268606" "ENST00000620710;ENST00000595583;ENST00000617846;ENST00000617505;ENST00000623806;ENST00000623438;ENST00000611557;ENST00000598543;ENST00000611674;ENST00000684311" "ENSP00000484290;ENSP00000470872;ENSP00000482879;ENSP00000483352;ENSP00000485541;ENSP00000485391;ENSP00000480738;ENSP00000469919;ENSP00000480491;ENSP00000507899" "P43356" "MAGEA2" "4101" "MAGE family member A2" "CT1.2;MAGE2;MAGEA2A" "Nucleus" "SwissProt" "ENSG00000271567" "ENST00000581164" "ENSP00000463419" "A0A075B759" "PPIAL4E" "730262" "peptidylprolyl isomerase A like 4E" "" "Cytosol" "DeepLoc2" From b41d9fe22f23dfc16df03712ffcc67191d8d2d51 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Wed, 25 Jan 2023 14:47:17 +0100 Subject: [PATCH 4/4] fix: update PMIDs and confident score --- 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 a98ea618..5e0bf5e0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -94632,10 +94632,10 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.6.5.3" - - references: "PMID:8443209" + - references: "PMID:27626371;PMID:12611891" - subsystem: - "Oxidative phosphorylation" - - confidence_score: 2 + - confidence_score: 4 - !!omap - id: "MAR03960" - name: "superoxide:superoxide oxidoreductase"