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Merge pull request #953 from SysBioChalmers/Fix-Transport_reactions_3
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Fix: GPR curation for transport reactions (3)
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@feiranl
feiranl authored Jan 13, 2025
2 parents c8d91ed + 3e9dec3 commit 1e02d01
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Showing 2 changed files with 16 additions and 51 deletions.
65 changes: 16 additions & 49 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -147986,7 +147986,7 @@
- MAM03134e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000113396 or ENSG00000121769 or ENSG00000130304 or ENSG00000135218 or ENSG00000143554 or ENSG00000145384 or ENSG00000163586 or ENSG00000164434 or ENSG00000164687 or ENSG00000167114 or ENSG00000170231 or ENSG00000170323 or ENSG00000197416 or ENSG00000205186"
- gene_reaction_rule: "ENSG00000121769 or ENSG00000130304 or ENSG00000135218 or ENSG00000143554 or ENSG00000145384 or ENSG00000163586 or ENSG00000164434 or ENSG00000164687 or ENSG00000167114 or ENSG00000170231 or ENSG00000170323 or ENSG00000197416 or ENSG00000205186"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -148149,7 +148149,6 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000165029"
- rxnFrom: "HMRdatabase"
- references: "PMID:16858612"
- subsystem:
Expand Down Expand Up @@ -170952,7 +170951,7 @@
- MAM02348m: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000012660 or ENSG00000026652 or ENSG00000100344 or ENSG00000102125 or ENSG00000111684 or ENSG00000123684 or ENSG00000125505 or ENSG00000141446 or ENSG00000143797 or ENSG00000151093 or ENSG00000160216 or ENSG00000169359 or ENSG00000170522 or ENSG00000171320 or ENSG00000176454 or ENSG00000186792 or ENSG00000197977"
- gene_reaction_rule: "ENSG00000151093 or ENSG00000169359 or ENSG00000171320"
- rxnFrom: "HMRdatabase"
- references: "PMID:14598172;PMID:6361812;PMID:8132483"
- subsystem:
Expand Down Expand Up @@ -174207,7 +174206,6 @@
- MAM01754m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174234,7 +174232,6 @@
- MAM01753m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174248,7 +174245,6 @@
- MAM01753m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174262,7 +174258,6 @@
- MAM01754m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174276,7 +174271,6 @@
- MAM01753m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174290,7 +174284,6 @@
- MAM01645m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174304,7 +174297,6 @@
- MAM01754m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174318,7 +174310,6 @@
- MAM01680m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174345,7 +174336,6 @@
- MAM01645m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174359,7 +174349,6 @@
- MAM01645m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174373,7 +174362,6 @@
- MAM01688m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174400,7 +174388,6 @@
- MAM01754m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174414,7 +174401,6 @@
- MAM01747m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174428,7 +174414,6 @@
- MAM01688m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174442,7 +174427,6 @@
- MAM01688m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174456,7 +174440,6 @@
- MAM01680m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand All @@ -174470,7 +174453,6 @@
- MAM01642m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000125454"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -175302,7 +175284,7 @@
- MAM02774x: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825"
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000185825"
- rxnFrom: "HMRdatabase"
- references: "PMID:18619829"
- subsystem:
Expand All @@ -175320,7 +175302,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825"
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000184343 or ENSG00000185825"
- rxnFrom: "HMRdatabase"
- references: "PMID:18619829"
- subsystem:
Expand All @@ -175338,7 +175320,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825"
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825"
- rxnFrom: "HMRdatabase"
- references: "PMID:18619829"
- subsystem:
Expand All @@ -175356,7 +175338,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825"
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130822 or ENSG00000185825"
- rxnFrom: "HMRdatabase"
- references: "PMID:18619829"
- subsystem:
Expand All @@ -175374,7 +175356,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130821 or ENSG00000130822 or ENSG00000184343 or ENSG00000185825"
- gene_reaction_rule: "ENSG00000067829 or ENSG00000067840 or ENSG00000101986 or ENSG00000130822 or ENSG00000185825"
- rxnFrom: "HMRdatabase"
- references: "PMID:18619829"
- subsystem:
Expand Down Expand Up @@ -175676,7 +175658,7 @@
- MAM02819x: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000100156 or ENSG00000108932 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190"
- gene_reaction_rule: "ENSG00000100156 or ENSG00000118596 or ENSG00000141526 or ENSG00000155380 or ENSG00000168679 or ENSG00000170190"
- rxnFrom: "HMRdatabase"
- references: "PMID:12739169;PMID:18305372"
- subsystem:
Expand Down Expand Up @@ -177132,7 +177114,6 @@
- MAM01365l: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000123643"
- rxnFrom: "HMRdatabase"
- references: "PMID:17466261;PMID:7718542;PMID:10049700;PMID:10072483;PMID:10391915;PMID:10574970;PMID:11004451;PMID:11311135;PMID:11389679;PMID:11557028;PMID:11564694;PMID:11742812;PMID:11827462;PMID:12117417;PMID:12824232;PMID:14574404;PMID:14770310;PMID:7690540;PMID:9751058;PMID:9759917;PMID:12883891;PMID:16288981;PMID:1904693;PMID:4424190;PMID:6432599;PMID:9868191;PMID:15465786;PMID:16082501"
- subsystem:
Expand Down Expand Up @@ -177170,7 +177151,6 @@
- MAM01628l: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000123643"
- rxnFrom: "HMRdatabase"
- references: "PMID:911815"
- subsystem:
Expand Down Expand Up @@ -177311,7 +177291,7 @@
- MAM03101l: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000104044 or ENSG00000123643"
- gene_reaction_rule: "ENSG00000104044"
- 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 @@ -179213,7 +179193,7 @@
- MAM03114g: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117620 or ENSG00000130958 or ENSG00000205060"
- gene_reaction_rule: "ENSG00000205060"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -179496,7 +179476,6 @@
- MAM01588g: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000107819"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -179950,7 +179929,7 @@
- MAM01252g: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000152779 or ENSG00000165449 or ENSG00000174327"
- gene_reaction_rule: "ENSG00000174327"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -180047,7 +180026,7 @@
- MAM03114g: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117620 or ENSG00000130958 or ENSG00000205060"
- gene_reaction_rule: "ENSG00000130958"
- rxnFrom: "HMRdatabase"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -188465,7 +188444,6 @@
- MAM02039e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000135917"
- rxnFrom: "Recon3D"
- references: "PMID:14770311;PMID:15623830"
- subsystem:
Expand Down Expand Up @@ -192760,7 +192738,6 @@
- MAM02403m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000103569"
- rxnFrom: "Recon3D"
- eccodes: "2.3.1.21"
- references: "PMID:12096044;PMID:16126913;PMID:9733774"
Expand Down Expand Up @@ -211144,7 +211121,6 @@
- MAM02770e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000115902"
- rxnFrom: "Recon3D"
- references: "PMID:14502423;PMID:11824937"
- subsystem:
Expand Down Expand Up @@ -211821,7 +211797,6 @@
- MAM02319e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000149150 or ENSG00000167703"
- rxnFrom: "Recon3D"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -212763,7 +212738,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000005471 or ENSG00000023839 or ENSG00000103222 or ENSG00000114770 or ENSG00000118777 or ENSG00000121270 or ENSG00000125257"
- gene_reaction_rule: "ENSG00000023839 or ENSG00000103222 or ENSG00000114770 or ENSG00000118777 or ENSG00000125257"
- rxnFrom: "Recon3D"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -236843,7 +236818,6 @@
- MAM02763e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000085563"
- rxnFrom: "Recon3D"
- references: "PMID:15290871"
- subsystem:
Expand Down Expand Up @@ -237414,7 +237388,6 @@
- MAM02823e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000112759 or ENSG00000174669"
- rxnFrom: "Recon3D"
- references: "PMID:20956085"
- subsystem:
Expand Down Expand Up @@ -237632,7 +237605,7 @@
- MAM01417e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000015520 or ENSG00000073060 or ENSG00000135218"
- gene_reaction_rule: "ENSG00000073060 or ENSG00000135218"
- rxnFrom: "Recon3D"
- subsystem:
- "Transport reactions"
Expand Down Expand Up @@ -242501,7 +242474,7 @@
- MAM03512e: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000023839 or ENSG00000073734 or ENSG00000108846 or ENSG00000125257"
- gene_reaction_rule: "ENSG00000023839 or ENSG00000108846 or ENSG00000125257"
- rxnFrom: "Recon3D"
- references: "PMID:25210150;PMID:26579438;PMID:23506869"
- subsystem:
Expand All @@ -242517,7 +242490,7 @@
- MAM03512e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000111700 or ENSG00000134538 or ENSG00000163959 or ENSG00000186198"
- gene_reaction_rule: "ENSG00000111700 or ENSG00000134538"
- rxnFrom: "Recon3D"
- references: "PMID:25210150;PMID:26579438"
- subsystem:
Expand Down Expand Up @@ -261877,9 +261850,6 @@
- !!omap
- id: "ENSG00000102100"
- name: "SLC35A2"
- !!omap
- id: "ENSG00000102125"
- name: "TAZ"
- !!omap
- id: "ENSG00000102144"
- name: "PGK1"
Expand Down Expand Up @@ -263077,9 +263047,6 @@
- !!omap
- id: "ENSG00000117600"
- name: "PLPPR4"
- !!omap
- id: "ENSG00000117620"
- name: "SLC35A3"
- !!omap
- id: "ENSG00000117643"
- name: "MAN1C1"
Expand Down
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