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fix: remove duplicate krebs cycle rxns of PDH and OGDH #541

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merged 7 commits into from
Apr 28, 2023
Merged

fix: remove duplicate krebs cycle rxns of PDH and OGDH #541

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9514724
fix-rxn: remove duplicated reactions MAR04137 and MAR05297
haowang-bioinfo Apr 21, 2023
60e7db5
fix-rxn: remove medium resolution version of PDH and OGDH
haowang-bioinfo Apr 24, 2023
b158eaf
fix: convert MAR08746 and MAM00561 from [c] to [m]
haowang-bioinfo Apr 24, 2023
e2868bc
fix: add new reaction MAM00561m + MAM02393m -> MAM02869m + MAM02984m
haowang-bioinfo Apr 24, 2023
9db0059
data: sync remove rxns to deprecated ids
haowang-bioinfo Apr 25, 2023
952ca0c
fix-gpr: modify GPRs for PDH reactions
haowang-bioinfo Apr 25, 2023
d095d98
fix-gpr: add E2 (DLAT) as subunit
haowang-bioinfo Apr 25, 2023
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4 changes: 4 additions & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -77,3 +77,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR08436" "R04125" "GCHOLAt" "" "" "" "GCCbim" "MNXR100068;MNXR100070" "HMR_8436" "RCR11319" "" 0 "" "RHEA:16945" "HMR_8436"
"MAR08437" "R03815" "GCHOLAt2" "" "" "" "GCCcm" "MNXR100069;MNXR100071" "HMR_8437" "RCR11320" "" 0 "" "" "HMR_8437"
"MAR03923" "R01221" "GLYCLm" "R01221C" "r0295" "" "r0295" "MNXR100330" "HMR_3923" "RCR10962" "" 0 "" "RHEA:27758" "HMR_3923"
"MAR04137" "R00209" "PDHm" "R00209C" "r0056" "" "PDHm" "MNXR102425" "HMR_4137" "RCR10275" "" 0 "RHEA:28043" "RHEA:28042" "HMR_4137"
"MAR05297" "R08549" "AKGDm" "" "r1114" "" "AKGDm" "MNXR95655" "HMR_5297" "RCR11671" "" 0 "" "" "HMR_5297"
"MAR06410" "R01699" "" "R01699M" "r0383" "" "r0383" "MNXR102427;MNXR107129" "HMR_6410" "RCR10446" "" 0 "" "RHEA:19189" "HMR_6410"
"MAR06411" "R01700" "" "" "r0384" "" "r0384" "MNXR107130;MNXR95657" "HMR_6411" "RCR10353" "" 0 "" "" "HMR_6411"
112 changes: 26 additions & 86 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7421,9 +7421,9 @@
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00561c"
- id: "MAM00561m"
- name: "2-(alpha-hydroxyethyl)thiamine-diphosphate"
- compartment: "c"
- compartment: "m"
- formula: "C14H20N4O8P2S"
- charge: -2
- inchis: ""
Expand Down Expand Up @@ -67697,26 +67697,6 @@
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- !!omap
- id: "MAR04137"
- name: "pyruvate:NAD+ 2-oxidoreductase (CoA-acetylating)"
- metabolites: !!omap
- MAM01261m: 1
- MAM01596m: 1
- MAM01597m: -1
- MAM02552m: -1
- MAM02553m: 1
- MAM02819m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000091140 and ENSG00000110435 and (ENSG00000131828 or ENSG00000163114) and ENSG00000150768 and ENSG00000168291"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.4.1;2.3.1.12;1.8.1.4;1.2.1.51"
- references: "PMID:11079566;PMID:2643922;PMID:8548923;PMID:2249846"
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- !!omap
- id: "MAR04281"
- name: "(S)-Lactate:NAD+ oxidoreductase"
Expand Down Expand Up @@ -68134,25 +68114,6 @@
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- !!omap
- id: "MAR06410"
- name: "pyruvate:[dihydrolipoyllysine-residue acetyltransferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-acetylating)"
- metabolites: !!omap
- MAM01596m: 1
- MAM02039m: -1
- MAM02393m: -1
- MAM02819m: -1
- MAM02869m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000131828 and ENSG00000168291) or (ENSG00000163114 and ENSG00000168291)"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.4.1"
- references: "PMID:18032470;PMID:2323578;PMID:2748588"
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- !!omap
- id: "MAR06412"
- name: "acetyl-CoA:enzyme N6-(dihydrolipoyl)lysine S-acetyltransferase"
Expand All @@ -68163,7 +68124,7 @@
- MAM02869m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000091140 and ENSG00000131828 and ENSG00000150768 and ENSG00000168291) or (ENSG00000091140 and ENSG00000150768 and ENSG00000163114 and ENSG00000168291)"
- gene_reaction_rule: "ENSG00000110435 and ENSG00000150768"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.3.1.12"
Expand Down Expand Up @@ -94552,45 +94513,6 @@
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR05297"
- name: "2-oxoglutarate:NAD+ 2-oxidoreductase (CoA-succinylating)"
- metabolites: !!omap
- MAM01306m: -1
- MAM01596m: 1
- MAM01597m: -1
- MAM02552m: -1
- MAM02553m: 1
- MAM02944m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000091140 and ENSG00000105953 and ENSG00000119689"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.4.2"
- references: "PMID:18004749;PMID:18206986;PMID:3207422"
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR06411"
- name: "2-oxoglutarate:[dihydrolipoyllysine-residue succinyltransferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-succinylating)"
- metabolites: !!omap
- MAM01306m: -1
- MAM01596m: 1
- MAM02039m: -1
- MAM02393m: -1
- MAM02934m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000105953 or ENSG00000181192 or ENSG00000197444"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.4.2"
- references: "PMID:10676873"
- subsystem:
- "Tricarboxylic acid cycle and glyoxylate/dicarboxylate metabolism"
- confidence_score: 0
- !!omap
- id: "MAR06413"
- name: ""
Expand Down Expand Up @@ -157975,11 +157897,11 @@
- id: "MAR08746"
- name: "pyruvate:thiamin diphosphate acetaldehydetransferase (decarboxylating)"
- metabolites: !!omap
- MAM00561c: 1
- MAM01596c: 1
- MAM02039c: -1
- MAM02819c: -1
- MAM02984c: -1
- MAM00561m: 1
- MAM01596m: 1
- MAM02039m: -1
- MAM02819m: -1
- MAM02984m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000131828 and ENSG00000168291) or (ENSG00000163114 and ENSG00000168291)"
Expand Down Expand Up @@ -306671,6 +306593,24 @@
- subsystem:
- "Fatty acid degradation"
- confidence_score: 0
- !!omap
- id: "MAR20069"
- name: "MAR20069"
- metabolites: !!omap
- MAM00561m: -1
- MAM02393m: -1
- MAM02869m: 1
- MAM02984m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000131828 and ENSG00000168291 and ENSG00000150768) or (ENSG00000163114 and ENSG00000168291 and ENSG00000150768)"
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- rxnNotes: ""
- rxnFrom: ""
- eccodes: ""
- references: ""
- subsystem:
- "Glycolysis / Gluconeogenesis"
- confidence_score: 0
- genes:
- !!omap
- id: "ENSG00000000419"
Expand Down
2 changes: 1 addition & 1 deletion model/metabolites.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -925,7 +925,7 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM00559c" "MAM00559" "1pyr5c" "C03912" "" "CHEBI:371" "1196" "" "" "HC01199" "1pyr5c" "MNXM1617" "m00559c" "m00559c"
"MAM00559m" "MAM00559" "1pyr5c" "C03912" "" "CHEBI:371" "1196" "" "" "HC01199" "1pyr5c" "MNXM1617" "m00559m" "m00559m"
"MAM00560c" "MAM00560" "ak2gchol_hs" "C05212" "" "CHEBI:36702" "" "" "" "" "ak2gchol_hs" "MNXM14173" "m00560c" "m00560c"
"MAM00561c" "MAM00561" "" "C05125" "" "CHEBI:978" "" "" "" "" "M00561" "MNXM1705" "m00561c" "m00561c"
"MAM00561m" "MAM00561" "" "C05125" "" "CHEBI:978" "" "" "" "" "M00561" "MNXM1705" "m00561c" "m00561c"
"MAM00562m" "MAM00562" "" "" "" "" "" "" "CE4797" "" "CE4797" "MNXM34616" "m00562m" "m00562m"
"MAM00563c" "MAM00563" "dmhptcoa" "" "" "" "" "" "CE4798" "" "CE4798" "MNXM163033;MNXM8044" "m00563c" "m00563c"
"MAM00563m" "MAM00563" "dmhptcoa" "" "" "" "" "" "CE4798" "" "CE4798" "MNXM163033;MNXM8044" "m00563m" "m00563m"
Expand Down
5 changes: 1 addition & 4 deletions model/reactions.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04099" "R00235" "ACSm" "R00235C" "r0067" "" "ACSm" "MNXR95413" "HMR_4099" "RCR10144" "" 0 "RHEA:23177" "RHEA:23176" "HMR_4099"
"MAR04108" "R00236" "" "R00236C" "r0068" "" "r0068" "MNXR105304" "HMR_4108" "RCR11020" "" 0 "" "" "HMR_4108"
"MAR04133" "R00316" "" "R00316C" "r0097" "" "r0097" "MNXR105307" "HMR_4133" "RCR11021" "" 0 "" "" "HMR_4133"
"MAR04137" "R00209" "PDHm" "R00209C" "r0056" "" "PDHm" "MNXR102425" "HMR_4137" "RCR10275" "" 0 "RHEA:28043" "RHEA:28042" "HMR_4137"
"MAR04281" "R00703" "" "R00703C" "r0173" "" "r0173" "MNXR101040" "HMR_4281" "RCR10083" "" 0 "" "RHEA:23444" "HMR_4281"
"MAR04388" "R00703" "LDH_L" "R00703C" "r0171" "" "LDH_L" "MNXR101040" "HMR_4388" "RCR10441" "" 0 "" "RHEA:23444" "HMR_4388"
"MAR04283" "R00711" "" "R00711C" "r0177" "" "ALDD2y" "MNXR95750" "HMR_4283" "RCR11022" "" 0 "RHEA:25299" "RHEA:25298" "HMR_4283"
Expand All @@ -29,7 +28,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04394" "R00299" "HEX1" "" "r0353" "" "HEX1" "MNXR100612" "HMR_4394" "RCR10145" "" 0 "" "RHEA:17825" "HMR_4394"
"MAR04396" "R08639" "PGMT" "R00959C" "r0621" "" "PGMT" "MNXR102528;MNXR102548" "HMR_4396" "RCR10146" "" 0 "" "" "HMR_4396"
"MAR04521" "R00303" "G6PPer" "" "r0396" "" "G6PPer" "MNXR99912" "HMR_4521" "RCR11028" "" 0 "" "RHEA:16689" "HMR_4521"
"MAR06410" "R01699" "" "R01699M" "r0383" "" "r0383" "MNXR102427;MNXR107129" "HMR_6410" "RCR10446" "" 0 "" "RHEA:19189" "HMR_6410"
"MAR06412" "R02569" "" "R02569C" "r0555" "" "r0555" "MNXR102430;MNXR107584" "HMR_6412" "RCR14187" "" 0 "" "RHEA:17017" "HMR_6412"
"MAR07745" "R01602" "" "" "" "" "HMR_7745" "MNXR107082" "HMR_7745" "RCR10447" "" 0 "RHEA:10267" "RHEA:10264" "HMR_7745"
"MAR07747" "R09086" "" "" "" "" "HMR_7747" "MNXR112530" "HMR_7747" "RCR10449" "" 0 "RHEA:11460" "RHEA:11461" "HMR_7747"
Expand Down Expand Up @@ -1349,8 +1347,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"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"
"MAR05297" "R08549" "AKGDm" "" "r1114" "" "AKGDm" "MNXR95655" "HMR_5297" "RCR11671" "" 0 "" "RHEA:27786" "HMR_5297"
"MAR06411" "R01700" "" "" "r0384" "" "r0384" "MNXR107130;MNXR95657" "HMR_6411" "RCR10353" "" 0 "" "" "HMR_6411"
"MAR06413" "R03316" "" "R03316M" "r0620" "" "r0620" "MNXR105357;MNXR108089" "HMR_6413" "RCR11672" "" 0 "" "" "HMR_6413"
"MAR06414" "R02570" "" "R02570C" "r0556" "" "r0556" "MNXR107585;MNXR95656" "HMR_6414" "RCR14482" "" 0 "" "RHEA:15213" "HMR_6414"
"MAR07704" "R00466" "GLXO2p" "" "" "" "GLXO2p" "MNXR100305" "HMR_7704" "RCR10605" "" 0 "" "RHEA:14837" "HMR_7704"
Expand Down Expand Up @@ -13075,3 +13071,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR20066" "R00009" "CAT;CATm;CATp;CATpp;CATr;R_CAT;R_CATm;R_CATp;R_CATpp;R_CATr" "" "" "" "" "MNXR96455" "" "" "" 0 "RHEA:20309" "" ""
"MAR20067" "" "" "" "" "" "" "MNXR133799" "" "" "" 0 "RHEA:55936" "" ""
"MAR20068" "" "" "" "" "" "" "MNXR171534" "" "" "" 0 "RHEA:60632" "" ""
"MAR20069" "" "" "" "" "" "" "" "" "" "" 0 "" "" ""