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fix: GPR curation for transport reactions (7) #957

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merged 3 commits into from
Jan 13, 2025
Merged

fix: GPR curation for transport reactions (7) #957

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6d672e4
fix: GPR curation for transport reactions (7)
JHL-452b Dec 30, 2024
c700a16
chore: add macaw test result
JHL-452b Dec 30, 2024
686b89c
Merge branch 'develop' into Fix-transport_reactions_7
feiranl Jan 13, 2025
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58 changes: 25 additions & 33 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -151628,7 +151628,7 @@
- MAM02184e: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000003989 or ENSG00000103257 or ENSG00000123643 or ENSG00000139514 or ENSG00000149150 or ENSG00000155465 or ENSG00000165349 or ENSG00000167703"
- gene_reaction_rule: "(ENSG00000092068 and ENSG00000168003) or ENSG00000103257 or ENSG00000123643 or ENSG00000149150 or ENSG00000155465 or ENSG00000167703"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:16288981;PMID:911815;PMID:10049700;PMID:10574970;PMID:11389679;PMID:11557028;PMID:11564694;PMID:12824232;PMID:14574404"
- subsystem:
Expand Down Expand Up @@ -151876,7 +151876,7 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000003989 or ENSG00000072041 or ENSG00000105281 or ENSG00000111371 or ENSG00000115902 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000174358"
- gene_reaction_rule: "ENSG00000072041 or ENSG00000105281 or ENSG00000111371 or ENSG00000115902 or ENSG00000134294 or ENSG00000139209 or ENSG00000174358"
- rxnFrom: "HMRdatabase"
- references: "PMID:12845534;PMID:10823827;PMID:11452978;PMID:15632147"
- subsystem:
Expand Down Expand Up @@ -151968,7 +151968,7 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000003989 or ENSG00000072041 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000168003 or ENSG00000174358"
- gene_reaction_rule: "ENSG00000072041 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000168003 or ENSG00000174358"
- rxnFrom: "HMRdatabase"
- references: "PMID:12930836;PMID:17322374"
- subsystem:
Expand Down Expand Up @@ -152026,7 +152026,7 @@
- MAM02724e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000003989 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000174358"
- gene_reaction_rule: "ENSG00000134294 or ENSG00000139209 or ENSG00000174358"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -152115,7 +152115,7 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000079215 or ENSG00000105143 or ENSG00000106688 or ENSG00000110436 or ENSG00000162383 or ENSG00000174358 or ENSG00000178537"
- gene_reaction_rule: "ENSG00000079215 or ENSG00000105143 or ENSG00000106688 or ENSG00000110436 or ENSG00000162383"
- rxnFrom: "HMRdatabase"
- references: "PMID:10823827"
- subsystem:
Expand Down Expand Up @@ -152466,7 +152466,7 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117834 or ENSG00000140675 or ENSG00000148942 or ENSG00000154025 or ENSG00000158865"
- gene_reaction_rule: "ENSG00000117834 or ENSG00000140675 or ENSG00000154025 or ENSG00000158865"
- rxnFrom: "HMRdatabase"
- references: "PMID:12748858"
- subsystem:
Expand Down Expand Up @@ -153595,7 +153595,7 @@
- MAM03089e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -153610,7 +153610,7 @@
- MAM03135e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -153625,7 +153625,7 @@
- MAM03089e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -153640,7 +153640,7 @@
- MAM03089e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -153655,7 +153655,7 @@
- MAM03089e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -153685,7 +153685,7 @@
- MAM02724e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -153700,7 +153700,7 @@
- MAM02724e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -153715,7 +153715,7 @@
- MAM02770e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -153730,7 +153730,7 @@
- MAM02724e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -153745,7 +153745,7 @@
- MAM03135e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -153760,7 +153760,7 @@
- MAM02993e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -153790,7 +153790,7 @@
- MAM02724e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000165029"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -153880,7 +153880,7 @@
- MAM03101e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257 or ENSG00000188687"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -154150,7 +154150,6 @@
- MAM02993e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -154165,7 +154164,6 @@
- MAM02770e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -154652,7 +154650,6 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -154686,7 +154683,6 @@
- MAM02993e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -154703,7 +154699,7 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -154771,7 +154767,7 @@
- MAM02896e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000105281 or ENSG00000115902"
- gene_reaction_rule: "ENSG00000105281 or ENSG00000115902"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -154788,7 +154784,7 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -154822,7 +154818,7 @@
- MAM02724e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -154856,7 +154852,7 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000105281 or ENSG00000115902"
- gene_reaction_rule: "ENSG00000105281 or ENSG00000115902"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand All @@ -154873,7 +154869,7 @@
- MAM02519e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
- gene_reaction_rule: "ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -154924,7 +154920,6 @@
- MAM03135e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103064 or ENSG00000103257"
- rxnFrom: "HMRdatabase"
- references: "PMID:14770309;PMID:14770310"
- subsystem:
Expand Down Expand Up @@ -265286,9 +265281,6 @@
- !!omap
- id: "ENSG00000148834"
- name: "GSTO1"
- !!omap
- id: "ENSG00000148942"
- name: "SLC5A12"
- !!omap
- id: "ENSG00000149016"
- name: "TUT1"
Expand Down
1 change: 0 additions & 1 deletion model/genes.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -1611,7 +1611,6 @@
"ENSG00000148795" "ENST00000638971;ENST00000638190;ENST00000369887;ENST00000640633;ENST00000638272;ENST00000639393;ENST00000469683;ENST00000489268" "ENSP00000492313;ENSP00000492539;ENSP00000358903;ENSP00000491508;ENSP00000492651" "P05093" "CYP17A1" "1586" "cytochrome P450 family 17 subfamily A member 1" "CPT7;CYP17;P450C17;S17AH" "Endoplasmic reticulum" "SwissProt"
"ENSG00000148832" "ENST00000357296;ENST00000278060;ENST00000356306;ENST00000476834;ENST00000480071;ENST00000483211;ENST00000529585;ENST00000368535;ENST00000528127;ENST00000530555" "ENSP00000349847;ENSP00000278060;ENSP00000348654;ENSP00000432737;ENSP00000435514;ENSP00000434550;ENSP00000432517" "Q6QHF9" "PAOX" "196743" "polyamine oxidase" "PAO" "Peroxisome;Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000148834" "ENST00000470554;ENST00000493946;ENST00000369713;ENST00000445155;ENST00000432659;ENST00000539281;ENST00000369710" "ENSP00000358727;ENSP00000406708;ENSP00000405325;ENSP00000441488;ENSP00000358724" "P78417" "GSTO1" "9446" "glutathione S-transferase omega 1" "GSTTLp28;P28" "Cytosol" "SwissProt"
"ENSG00000148942" "ENST00000396005;ENST00000527405;ENST00000280467;ENST00000533617;ENST00000528822" "ENSP00000379326;ENSP00000436011;ENSP00000280467;ENSP00000435053" "Q1EHB4" "SLC5A12" "159963" "solute carrier family 5 member 12" "MGC52019;SMCT2" "Nucleus" "CellAtlas"
"ENSG00000149016" "ENST00000308436;ENST00000476907;ENST00000469480;ENST00000463241;ENST00000278279;ENST00000494385;ENST00000478537" "ENSP00000308000;ENSP00000419607;ENSP00000278279;ENSP00000420739;ENSP00000419792" "Q9H6E5" "TUT1" "64852" "terminal uridylyl transferase 1, U6 snRNA-specific" "FLJ21850;FLJ22267;FLJ22347;PAPD2;RBM21;TENT1;TUTase" "Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000149084" "ENST00000278353;ENST00000527433;ENST00000531185;ENST00000636007;ENST00000395700;ENST00000636722;ENST00000637401;ENST00000638034;ENST00000527213;ENST00000532178;ENST00000533090;ENST00000533802;ENST00000534053;ENST00000525736" "ENSP00000278353;ENSP00000490749;ENSP00000436582;ENSP00000490822;ENSP00000379052;ENSP00000490003;ENSP00000490421;ENSP00000490701" "Q53GQ0" "HSD17B12" "51144" "hydroxysteroid 17-beta dehydrogenase 12" "KAR;SDR12C1" "Endoplasmic reticulum" "SwissProt"
"ENSG00000149089" "ENST00000532428;ENST00000395787;ENST00000527830" "ENSP00000474191;ENSP00000379133" "Q96GX9" "APIP" "51074" "APAF1 interacting protein" "APIP2;CGI-29;Mmrp19" "Nucleus;Cytosol" "SwissProt;CellAtlas"
Expand Down
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