Merge pull request #462 from SysBioChalmers/fix/addCIsubunit

fix: add subunit NDUFA7 to complex I
SysBioChalmers · Jan 26, 2023 · 075737e · 075737e
2 parents 5f42877 + b41d9fe
commit 075737e
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 7 deletions.
diff --git 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"
@@ -94628,14 +94628,14 @@
           - 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"
-      - references: "PMID:8443209"
+      - references: "PMID:27626371;PMID:12611891"
       - subsystem:
           - "Oxidative phosphorylation"
-      - confidence_score: 2
+      - confidence_score: 4
     - !!omap
       - id: "MAR03960"
       - name: "superoxide:superoxide oxidoreductase"
@@ -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"

diff --git 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"	""	"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"