Merge pull request #489 from SysBioChalmers/fix/modifyMitoComplexGPR

fix: modify GPR rules of mitochondrial complexes II, IV, and V
SysBioChalmers · Mar 3, 2023 · d6f92a3 · d6f92a3
2 parents 2fd3d7c + c3faf5b
commit d6f92a3
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Showing 2 changed files with 10 additions and 4 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: "2023-02-21"
+    date: "2023-02-28"
     authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas"
     email: "jonrob@chalmers.se"
     organization: "Chalmers University of Technology"
@@ -94476,7 +94476,7 @@
           - MAM03103m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000105379 or ENSG00000140374 or ENSG00000143252 or ENSG00000171503"
+      - gene_reaction_rule: "ENSG00000073578 and ENSG00000117118 and ENSG00000143252 and ENSG00000204370"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.5.5.1"
@@ -94514,7 +94514,7 @@
           - MAM02630m: -1
       - 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: "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"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.9.3.1"
@@ -94534,7 +94534,7 @@
           - MAM02751m: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000099624 and ENSG00000110955 and ENSG00000116459 and ENSG00000124172 and ENSG00000135390 and ENSG00000152234 and ENSG00000154518 and ENSG00000154723 and ENSG00000156411 and ENSG00000159199 and ENSG00000165629 and ENSG00000167283 and ENSG00000167863 and ENSG00000169020 and ENSG00000173915 and ENSG00000198899 and ENSG00000228253 and ENSG00000241468 and ENSG00000241837"
+      - gene_reaction_rule: "ENSG00000099624 and ENSG00000110955 and ENSG00000116459 and ENSG00000124172 and ENSG00000135390 and ENSG00000152234 and ENSG00000154518 and ENSG00000154723 and ENSG00000156411 and ENSG00000159199 and ENSG00000165629 and ENSG00000167283 and ENSG00000167863 and ENSG00000169020 and ENSG00000173915 and ENSG00000198899 and ENSG00000228253 and ENSG00000241468 and ENSG00000241837 and ENSG00000249222 and ENSG00000180389"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.6.1.3;3.6.1.5;3.6.3.1;3.6.3.10;3.6.3.14;3.6.3.8;3.6.3.9;3.6.4.3;3.6.4.4;3.6.4.6;3.6.4.12;3.6.4.13"
@@ -309839,6 +309839,8 @@
       - id: "ENSG00000180233"
     - !!omap
       - id: "ENSG00000180251"
+    - !!omap
+      - id: "ENSG00000180389"
     - !!omap
       - id: "ENSG00000180432"
     - !!omap
@@ -310709,6 +310711,8 @@
       - id: "ENSG00000248144"
     - !!omap
       - id: "ENSG00000248933"
+    - !!omap
+      - id: "ENSG00000249222"
     - !!omap
       - id: "ENSG00000249853"
     - !!omap

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -2430,6 +2430,7 @@ genes	geneENSTID	geneENSPID	geneUniProtID	geneSymbols	geneEntrezID	geneNames	gen
 "ENSG00000180210"	"ENST00000311907;ENST00000469189;ENST00000530231;ENST00000442468;ENST00000490274"	"ENSP00000308541;ENSP00000433907;ENSP00000387413"	"P00734"	"F2"	"2147"	"coagulation factor II, thrombin"	""	"Extracellular"	"DeepLoc2"
 "ENSG00000180233"	"ENST00000323037;ENST00000459998"	"ENSP00000323879"	"Q8NHG8"	"ZNRF2"	"223082"	"zinc and ring finger 2"	"RNF202"	"Nucleus;Lysosome"	"SwissProt;CellAtlas"
 "ENSG00000180251"	"ENST00000295269;ENST00000492154"	"ENSP00000295269"	"Q6AI14"	"SLC9A4"	"389015"	"solute carrier family 9 member A4"	"NHE4"	"Nucleus"	"CellAtlas"
+"ENSG00000180389"	"ENST00000381026"	""	"Q5VTU8"	"ATP5F1EP2"	"432369"	"ATP synthase F1 subunit epsilon pseudogene 2"	"ATP5EP2"	"Inner mitochondria"	"SwissProt"
 "ENSG00000180432"	"ENST00000437102;ENST00000316161"	"ENSP00000404499;ENSP00000318867"	"Q9UNU6"	"CYP8B1"	"1582"	"cytochrome P450 family 8 subfamily B member 1"	"CYP12"	"Endoplasmic reticulum"	"SwissProt"
 "ENSG00000180537"	"ENST00000488763;ENST00000488300;ENST00000420478;ENST00000471906;ENST00000423553;ENST00000537663;ENST00000544682;ENST00000537388"	"ENSP00000417500;ENSP00000420465;ENSP00000419329;ENSP00000417514;ENSP00000418717;ENSP00000443228;ENSP00000442021;ENSP00000441271"	"Q8N6D2"	"RNF182"	"221687"	"ring finger protein 182"	"MGC33993"	"Golgi apparatus;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000180549"	"ENST00000314412"	"ENSP00000318142"	"Q11130"	"FUT7"	"2529"	"fucosyltransferase 7"	""	"Golgi apparatus"	"SwissProt;CellAtlas"
@@ -2865,6 +2866,7 @@ genes	geneENSTID	geneENSPID	geneUniProtID	geneSymbols	geneEntrezID	geneNames	gen
 "ENSG00000248098"	"ENST00000538423;ENST00000269980;ENST00000542943;ENST00000457836;ENST00000541315;ENST00000535632;ENST00000545787;ENST00000544905"	"ENSP00000269980;ENSP00000440345;ENSP00000416000;ENSP00000445809;ENSP00000445727"	"P12694"	"BCKDHA"	"593"	"branched chain keto acid dehydrogenase E1 subunit alpha"	"MSU;OVD1A"	"Mitochondria"	"SwissProt"
 "ENSG00000248144"	"ENST00000515683;ENST00000510055;ENST00000511397;ENST00000505942"	"ENSP00000426083;ENSP00000478439;ENSP00000478545"	"P00326"	"ADH1C"	"126"	"alcohol dehydrogenase 1C (class I), gamma polypeptide"	"ADH3"	"Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000248933"	"ENST00000511280"	"ENSP00000423115"	"D6RA61"	"USP17L22"	"100287513"	"ubiquitin specific peptidase 17 like family member 22"	""	"Cytosol;Nucleus"	"DeepLoc2"
+"ENSG00000249222"	"ENST00000505920"	"ENSP00000421076"	"Q7Z4Y8"	"ATP5MGL"	"267020"	"ATP synthase membrane subunit g like"	"ATP5K2;ATP5L2"	"Inner mitochondria"	"SwissProt"
 "ENSG00000249853"	"ENST00000312719;ENST00000441954"	"ENSP00000427888"	"Q8IZT8"	"HS3ST5"	"222537"	"heparan sulfate-glucosamine 3-sulfotransferase 5"	"3-OST-5"	"Golgi apparatus"	"SwissProt"
 "ENSG00000249948"	"ENST00000508166;ENST00000503442;ENST00000511446;ENST00000504802;ENST00000508264;ENST00000613293;ENST00000610628"	"ENSP00000427458;ENSP00000422220;ENSP00000423754;ENSP00000480447;ENSP00000478226"	""	"GBA3"	"57733"	"glucosylceramidase beta 3 (gene/pseudogene)"	"GLUC;KLrP"	""	""
 "ENSG00000250565"	"ENST00000524249;ENST00000306448;ENST00000522587;ENST00000524188;ENST00000505245;ENST00000522219"	"ENSP00000304891;ENSP00000428141"	"Q96A05"	"ATP6V1E2"	"90423"	"ATPase H+ transporting V1 subunit E2"	"ATP6E1;ATP6EL2;ATP6V1EL2;MGC9341;VMA4"	"Cytosol"	"DeepLoc2"