Merge pull request #941 from SysBioChalmers/Fix_Arg_Pro_Tyr_metabolism

Fix: GPR curation for Arg_Pro_Tyr_metabolism
SysBioChalmers · Jan 13, 2025 · f142917 · f142917
2 parents a09acc1 + 8ce6988
commit f142917
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Showing 2 changed files with 9 additions and 18 deletions.
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -69540,7 +69540,6 @@
           - MAM02039m: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000142920"
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.1.1.19"
       - references: "PMID:10800966;PMID:14738999"
@@ -70381,7 +70380,7 @@
           - MAM02921c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000064763 or ENSG00000118514 or ENSG00000197601"
+      - gene_reaction_rule: "ENSG00000197601"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.1.-"
       - references: "PMID:7040832;PMID:10047787"
@@ -70399,7 +70398,7 @@
           - MAM02922c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000064763 or ENSG00000118514 or ENSG00000197601"
+      - gene_reaction_rule: "ENSG00000118514 or ENSG00000197601"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.1.-"
       - references: "PMID:7040832;PMID:10047787"
@@ -70646,7 +70645,7 @@
           - MAM02925c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000064763 or ENSG00000118514 or ENSG00000197601"
+      - gene_reaction_rule: "ENSG00000118514 or ENSG00000197601"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.1.-"
       - references: "PMID:10047787;PMID:7040832"
@@ -72915,7 +72914,6 @@
           - MAM02152c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000117305"
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.4.1.22"
       - subsystem:
@@ -72970,7 +72968,7 @@
           - MAM02720c: 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"
       - rxnFrom: "HMRdatabase"
       - eccodes:
           - "1.2.1.5"
@@ -72991,7 +72989,7 @@
           - MAM02720m: 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"
       - rxnFrom: "HMRdatabase"
       - eccodes:
           - "1.2.1.5"
@@ -73012,7 +73010,7 @@
           - MAM02720c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
+      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.1.5"
       - references: "PMID:17379813;PMID:18621017"
@@ -73031,7 +73029,7 @@
           - MAM02720m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
+      - gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.2.1.5"
       - references: "PMID:17379813;PMID:18621017"
@@ -73193,7 +73191,7 @@
           - 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 ENSG00000248144"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.1"
       - subsystem:
@@ -73334,7 +73332,6 @@
           - MAM02630c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000077498"
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.14.18.1"
       - subsystem:
@@ -200664,7 +200661,7 @@
           - MAM02041l: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000005381 or ENSG00000117592"
+      - gene_reaction_rule: "ENSG00000005381"
       - rxnFrom: "Recon3D"
       - eccodes: "1.11.1.7"
       - references: "PMID:9164836"
@@ -239809,7 +239806,6 @@
           - MAM03564c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108"
       - rxnFrom: "Recon3D"
       - eccodes: "2.4.1.17"
       - references: "PMID:19116261"
@@ -239827,7 +239823,6 @@
           - MAM03563c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108"
       - rxnFrom: "Recon3D"
       - eccodes: "2.4.1.17"
       - references: "PMID:23683503"
@@ -264722,9 +264717,6 @@
     - !!omap
       - id: "ENSG00000142892"
       - name: "PIGK"
-    - !!omap
-      - id: "ENSG00000142920"
-      - name: "AZIN2"
     - !!omap
       - id: "ENSG00000142973"
       - name: "CYP4B1"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -1469,7 +1469,6 @@
 "ENSG00000142623"	"ENST00000375471;ENST00000483501;ENST00000648847;ENST00000460293"	"ENSP00000364620"	"Q9ULC6"	"PADI1"	"29943"	"peptidyl arginine deiminase 1"	"HPAD10;PAD1;PDI;PDI1"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000142657"	"ENST00000491493;ENST00000487775;ENST00000270776;ENST00000477958;ENST00000483936;ENST00000465632;ENST00000460189;ENST00000493288;ENST00000498356;ENST00000496718"	"ENSP00000466358;ENSP00000270776;ENSP00000465311;ENSP00000466156;ENSP00000466574;ENSP00000467362"	"P52209"	"PGD"	"5226"	"phosphogluconate dehydrogenase"	""	"Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000142892"	"ENST00000370812;ENST00000445065;ENST00000487906;ENST00000359130;ENST00000478391"	"ENSP00000359848;ENSP00000388854;ENSP00000474518;ENSP00000352041"	"Q92643"	"PIGK"	"10026"	"phosphatidylinositol glycan anchor biosynthesis class K"	"GPI8;hGPI8"	"Endoplasmic reticulum"	"SwissProt"
-"ENSG00000142920"	"ENST00000478635;ENST00000481886;ENST00000475935;ENST00000294517;ENST00000462920;ENST00000471119;ENST00000495135;ENST00000477570;ENST00000483027;ENST00000492420;ENST00000373443;ENST00000497710;ENST00000473089;ENST00000652171;ENST00000484656;ENST00000373440;ENST00000652381;ENST00000373441;ENST00000478204;ENST00000497280;ENST00000492521"	"ENSP00000294517;ENSP00000362542;ENSP00000498229;ENSP00000362539;ENSP00000362540"	"Q96A70"	"AZIN2"	"113451"	"antizyme inhibitor 2"	"ADC;KIAA1945;ODC-p;ODC1L;ODCp"	"Endoplasmic reticulum;Golgi apparatus;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000142973"	"ENST00000546128;ENST00000413093;ENST00000640628;ENST00000534708;ENST00000271153;ENST00000371923;ENST00000529715;ENST00000464439;ENST00000371919;ENST00000614163;ENST00000526297;ENST00000452782;ENST00000468637;ENST00000481248;ENST00000497005"	"ENSP00000492115;ENSP00000433367;ENSP00000271153;ENSP00000360991;ENSP00000443212;ENSP00000433068;ENSP00000360987;ENSP00000484629;ENSP00000438995"	"P13584"	"CYP4B1"	"1580"	"cytochrome P450 family 4 subfamily B member 1"	""	"Endoplasmic reticulum"	"SwissProt"
 "ENSG00000143036"	"ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000422520;ENST00000532427;ENST00000475883;ENST00000530397;ENST00000532670"	"ENSP00000389143;ENSP00000271227;ENSP00000433641;ENSP00000431836;ENSP00000432789;ENSP00000410832;ENSP00000436661;ENSP00000434457;ENSP00000432880"	"Q8N4M1"	"SLC44A3"	"126969"	"solute carrier family 44 member 3"	"CTL3;MGC45474"	"Cell membrane"	"DeepLoc2"
 "ENSG00000143149"	"ENST00000354775;ENST00000463610;ENST00000491436;ENST00000461664;ENST00000471457"	"ENSP00000346827"	"P49189"	"ALDH9A1"	"223"	"aldehyde dehydrogenase 9 family member A1"	"ALDH4;ALDH7;ALDH9;E3"	"Cytosol"	"SwissProt;CellAtlas"