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Merge pull request #525 from SysBioChalmers/fix/modifyIDHgprs
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fix: refine reactions, reversibility, and GPRs of Isocitrate Dehydrogenase metabolism
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@haowang-bioinfo
haowang-bioinfo authored Apr 6, 2023
2 parents 0b1bd42 + bab19bb commit be8998b
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Showing 3 changed files with 18 additions and 148 deletions.
7 changes: 7 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -63,3 +63,10 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR06710" "" "" "RE2477C" "" "" "RE2477C" "MNXR103685" "HMR_6710" "RCR11403" "" 0 "" "" "HMR_6710"
"MAR06737" "" "" "RE2384C" "" "" "RE2384C" "MNXR103663" "HMR_6737" "RCR14365" "" 0 "" "" "HMR_6737"
"MAR04279" "R00104" "NADK" "R00104C" "" "" "" "MNXR101882" "HMR_4279" "RCR10008" "" 0 "RHEA:18630" "RHEA:18629" "HMR_4279"
"MAR04111" "R00268" "" "R00268C" "r0082" "" "r0082" "MNXR105305" "HMR_4111" "RCR10601" "" 0 "" "RHEA:19381" "HMR_4111"
"MAR04112" "R00268" "" "R00268C" "r0083" "" "r0083" "MNXR105305" "HMR_4112" "RCR11659" "" 0 "" "RHEA:19381" "HMR_4112"
"MAR04113" "R00268" "" "R00268C" "r0084" "" "r0084" "MNXR105305" "HMR_4113" "RCR10602" "" 0 "" "RHEA:19381" "HMR_4113"
"MAR04585" "R01899" "" "R01899C" "r0422" "" "r0422" "MNXR105340" "HMR_4585" "RCR11667" "" 0 "" "RHEA:25588" "HMR_4585"
"MAR04586" "R01899" "" "R01899C" "r0423" "" "r0423" "MNXR105340" "HMR_4586" "RCR11668" "" 0 "" "RHEA:25588" "HMR_4586"
"MAR04587" "R01899" "" "R01899C" "r0424" "" "r0424" "MNXR105340" "HMR_4587" "RCR10604" "" 0 "" "RHEA:25588" "HMR_4587"
"MAR04588" "" "" "" "r0425" "" "r0425" "MNXR105341" "HMR_4588" "RCR11669" "" 0 "" "" "HMR_4588"
144 changes: 7 additions & 137 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -93604,9 +93604,9 @@
- MAM02183c: -1
- MAM02554c: -1
- MAM02555c: 1
- lower_bound: 0
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- gene_reaction_rule: "ENSG00000138413"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
Expand Down Expand Up @@ -93643,7 +93643,7 @@
- MAM02553m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000067829 or ENSG00000101365 or ENSG00000166411"
- gene_reaction_rule: "ENSG00000067829 and ENSG00000101365 and ENSG00000166411"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.41"
Expand All @@ -93660,70 +93660,16 @@
- MAM02183m: -1
- MAM02554m: -1
- MAM02555m: 1
- lower_bound: 0
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- gene_reaction_rule: "ENSG00000182054"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
- references: ""
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04111"
- name: "oxalosuccinate carboxy-lyase (2-oxoglutarate-forming)"
- metabolites: !!omap
- MAM01306c: 1
- MAM01596c: 1
- MAM02039c: -1
- MAM02662c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
- references: "PMID:16489927;PMID:9866202"
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04112"
- name: "oxalosuccinate carboxy-lyase (2-oxoglutarate-forming)"
- metabolites: !!omap
- MAM01306m: 1
- MAM01596m: 1
- MAM02039m: -1
- MAM02662m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
- references: "PMID:16489927;PMID:9866202"
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04113"
- name: "oxalosuccinate carboxy-lyase (2-oxoglutarate-forming)"
- metabolites: !!omap
- MAM01306x: 1
- MAM01596x: 1
- MAM02039x: -1
- MAM02662x: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
- references: "PMID:16489927;PMID:9866202"
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04139"
- name: "(S)-malate:NAD+ oxidoreductase"
Expand Down Expand Up @@ -93964,82 +93910,6 @@
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04585"
- name: "Isocitrate:NADP+ oxidoreductase"
- metabolites: !!omap
- MAM02039c: -1
- MAM02183c: 1
- MAM02554c: 1
- MAM02555c: -1
- MAM02662c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
- references: "PMID:10521434;PMID:16489927;PMID:9866202"
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04586"
- name: "Isocitrate:NADP+ oxidoreductase"
- metabolites: !!omap
- MAM02039m: -1
- MAM02183m: 1
- MAM02554m: 1
- MAM02555m: -1
- MAM02662m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
- references: "PMID:10521434;PMID:16489927;PMID:9866202"
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04587"
- name: "Isocitrate:NADP+ oxidoreductase"
- metabolites: !!omap
- MAM02039x: -1
- MAM02183x: 1
- MAM02554x: 1
- MAM02555x: -1
- MAM02662x: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
- references: "PMID:10521434;PMID:16489927;PMID:9866202"
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04588"
- name: ""
- metabolites: !!omap
- MAM02039m: -1
- MAM02183m: 1
- MAM02552m: 1
- MAM02553m: -1
- MAM02662m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
- references: "PMID:10521434;PMID:16489927;PMID:18484410;PMID:9866202"
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR04589"
- name: "isocitrate hydro-lyase (cis-aconitate-forming)"
Expand Down Expand Up @@ -150129,9 +149999,9 @@
- MAM02183x: -1
- MAM02554x: -1
- MAM02555x: 1
- lower_bound: 0
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138413 or ENSG00000182054"
- gene_reaction_rule: "ENSG00000138413"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.42"
Expand Down
15 changes: 4 additions & 11 deletions model/reactions.tsv
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Expand Up @@ -1333,13 +1333,10 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR08667" "" "MECOALm" "" "" "" "MECOALm" "MNXR101452" "HMR_8667" "RCR11654" "" 0 "" "" "HMR_8667"
"MAR08668" "" "MECOAS1m" "" "" "" "MECOAS1m" "MNXR101453" "HMR_8668" "RCR11655" "" 0 "" "" "HMR_8668"
"MAR08669" "" "MESCOALm" "" "" "" "MESCOALm" "MNXR101469" "HMR_8669" "RCR11656" "" 0 "" "" "HMR_8669"
"MAR00710" "R00267" "ICDHyr" "" "" "" "ICDHy" "MNXR100781" "HMR_0710" "RCR11657" "" 0 "" "RHEA:19629" "HMR_0710"
"MAR00710" "R00267" "ICDHyr" "" "" "" "ICDHy" "MNXR100781" "HMR_0710" "RCR11657" "" 0 "RHEA:19632" "RHEA:19629" "HMR_0710"
"MAR03787" "R00410" "OCOAT1m" "" "" "R-HSA-74177" "OCOAT1m" "MNXR102148" "HMR_3787" "RCR11658" "" 0 "RHEA:25481" "RHEA:25480" "HMR_3787"
"MAR03957" "R00709" "ICDHxm" "" "" "" "ICDHxm" "MNXR100782" "HMR_3957" "RCR10349" "" 0 "" "RHEA:23632" "HMR_3957"
"MAR03958" "R00267" "ICDHym" "" "" "" "ICDHyrm" "MNXR100781" "HMR_3958" "RCR10350" "" 0 "" "RHEA:19629" "HMR_3958"
"MAR04111" "R00268" "" "R00268C" "r0082" "" "r0082" "MNXR105305" "HMR_4111" "RCR10601" "" 0 "" "RHEA:19381" "HMR_4111"
"MAR04112" "R00268" "" "R00268C" "r0083" "" "r0083" "MNXR105305" "HMR_4112" "RCR11659" "" 0 "" "RHEA:19381" "HMR_4112"
"MAR04113" "R00268" "" "R00268C" "r0084" "" "r0084" "MNXR105305" "HMR_4113" "RCR10602" "" 0 "" "RHEA:19381" "HMR_4113"
"MAR03957" "R00709" "ICDHxm" "" "" "" "ICDHxm" "MNXR100782" "HMR_3957" "RCR10349" "" 0 "RHEA:23633" "RHEA:23632" "HMR_3957"
"MAR03958" "R00267" "ICDHym" "" "" "" "ICDHyrm" "MNXR100781" "HMR_3958" "RCR10350" "" 0 "RHEA:19632" "RHEA:19629" "HMR_3958"
"MAR04139" "R00342" "MDH" "R00342C" "r0104" "" "MDH" "MNXR101439" "HMR_4139" "RCR10164" "" 0 "" "RHEA:21432" "HMR_4139"
"MAR04141" "R00342" "MDHm" "R00342C" "r0105" "" "MDHm" "MNXR101439" "HMR_4141" "RCR11660" "" 0 "RHEA:21435" "RHEA:21432" "HMR_4141"
"MAR04145" "R00351" "CSm" "R00351M" "r0107" "" "CSm" "MNXR96920" "HMR_4145" "RCR11661" "" 0 "RHEA:16848" "RHEA:16845" "HMR_4145"
Expand All @@ -1353,10 +1350,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04456" "R01324" "ACONTm" "R01324C" "r0316" "" "ACONTm" "MNXR95384" "HMR_4456" "RCR10351" "" 0 "" "RHEA:10336" "HMR_4456"
"MAR04458" "R01325" "" "R01325C" "r0317" "" "r0317" "MNXR105321;MNXR95386" "HMR_4458" "RCR10106" "" 0 "RHEA:10231" "RHEA:10228" "HMR_4458"
"MAR04465" "R01392" "HPYRRy" "R01392C" "r0327" "" "HPYRRy" "MNXR100336" "HMR_4465" "RCR11666" "" 0 "" "RHEA:18657" "HMR_4465"
"MAR04585" "R01899" "" "R01899C" "r0422" "" "r0422" "MNXR105340" "HMR_4585" "RCR11667" "" 0 "" "RHEA:25588" "HMR_4585"
"MAR04586" "R01899" "" "R01899C" "r0423" "" "r0423" "MNXR105340" "HMR_4586" "RCR11668" "" 0 "" "RHEA:25588" "HMR_4586"
"MAR04587" "R01899" "" "R01899C" "r0424" "" "r0424" "MNXR105340" "HMR_4587" "RCR10604" "" 0 "" "RHEA:25588" "HMR_4587"
"MAR04588" "" "" "" "r0425" "" "r0425" "MNXR105341" "HMR_4588" "RCR11669" "" 0 "" "" "HMR_4588"
"MAR04589" "R01900" "" "R01900C" "r0426" "" "r0426" "MNXR105342;MNXR95387" "HMR_4589" "RCR10352" "" 0 "" "RHEA:22144" "HMR_4589"
"MAR04652" "R02164" "r0509" "R02164C" "r0509" "" "r0509" "MNXR107340" "HMR_4652" "RCR14481" "" 0 "" "RHEA:13713" "HMR_4652"
"MAR05294" "R00362" "" "R00362C" "r1109" "" "r1109" "MNXR96731" "HMR_5294" "RCR11670" "" 0 "RHEA:10761" "RHEA:10760" "HMR_5294"
Expand Down Expand Up @@ -4345,7 +4338,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR08333" "" "FUT99g" "" "" "" "FUT97g" "MNXR99763" "HMR_8333" "RCR13741" "" 0 "" "" "HMR_8333"
"MAR08334" "R06230" "G12MT1_L" "" "" "" "FUT98g" "MNXR99768" "HMR_8334" "RCR13742" "" 0 "" "" "HMR_8334"
"MAR08337" "R06037" "ST3GAL62g" "" "" "" "ST3GAL62g" "MNXR104553" "HMR_8337" "RCR13743" "" 0 "" "" "HMR_8337"
"MAR00712" "R00267" "" "" "" "R-HSA-389550" "ICDHyp" "MNXR115983" "HMR_0712" "RCR10264" "" 0 "" "RHEA:19629" "HMR_0712"
"MAR00712" "R00267" "" "" "" "R-HSA-389550" "ICDHyp" "MNXR115983" "HMR_0712" "RCR10264" "" 0 "RHEA:19632" "RHEA:19629" "HMR_0712"
"MAR03992" "R00100" "" "R00100C" "r0023" "" "r0023" "MNXR106388" "HMR_3992" "RCR10928" "" 0 "" "RHEA:46680" "HMR_3992"
"MAR04228" "R02665" "3HAO" "R02665C" "r0562" "" "3HAO" "MNXR94889" "HMR_4228" "RCR10929" "" 0 "" "RHEA:17953" "HMR_4228"
"MAR04251" "R03348" "NNDPR" "R03348C" "r0623" "" "NNDPR" "MNXR101980" "HMR_4251" "RCR14666" "" 0 "RHEA:12735" "RHEA:12733" "HMR_4251"
Expand Down

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