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fix: refine Trp metabolism reactions and GPRs #708

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merged 6 commits into from
Oct 16, 2023
+15 −58
Merged

fix: refine Trp metabolism reactions and GPRs #708

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dcc2690
fix: remove ENSG00000159423 from MAR00051
haowang-bioinfo Oct 14, 2023
1eb71c6
fix: remove MAR08564 and MAR08565
haowang-bioinfo Oct 14, 2023
f739d41
fix: remove ENSG00000109576 from MAR04222
haowang-bioinfo Oct 14, 2023
34c2da9
doc: sync deletion of MAR08564+MAR08565 to data files
haowang-bioinfo Oct 14, 2023
e503177
fix/doc: make MAR04222 and MAR02765 irreversible based on Uniprot
haowang-bioinfo Oct 14, 2023
ca672c9
doc: sync deletion of MAM00926c
haowang-bioinfo Oct 14, 2023
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1 change: 1 addition & 0 deletions data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Expand Up @@ -2247,3 +2247,4 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM02757l" "MAM02757" "" "" "" "" "" "" "" "" "M02757" "" "m02757l" "m02757l"
"MAM02757n" "MAM02757" "" "" "" "" "" "" "" "" "M02757" "" "m02757n" "m02757n"
"MAM01816n" "MAM01816" "" "" "" "" "" "PROTEIN" "" "" "M01816" "" "m01816n" "m01816n"
"MAM00926c" "MAM00926" "4aphdob" "C01252" "HMDB0000978" "CHEBI:17442" "472" "" "" "" "4aphdob" "MNXM163204" "m00926c" "m00926c"
4 changes: 3 additions & 1 deletion data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -238,4 +238,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR07771" "" "NADtpu" "" "" "" "NADtx" "MNXR101881" "HMR_7771" "RCR20023" "" 0 "" "" "HMR_7771"
"MAR07782" "" "ADPtx" "" "" "" "ADPtx" "MNXR95484" "HMR_7782" "RCR20201" "" 0 "" "" "HMR_7782"
"MAR07783" "" "AMPtp" "" "" "" "AMPtp" "MNXR95830" "HMR_7783" "RCR20046" "" 0 "" "" "HMR_7783"
"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790"
"MAR07790" "" "FADtx" "" "" "" "FADtx" "MNXR99217" "HMR_7790" "RCR20203" "" 0 "" "" "HMR_7790"
"MAR08564" "" "KYNAKGAT" "" "" "" "KYNAKGAT" "MNXR100948" "HMR_8564" "RCR11356" "" 0 "" "" "HMR_8564"
"MAR08565" "R03445" "KYNATESYN" "" "" "" "KYNATESYN" "MNXR100949" "HMR_8565" "RCR11357" "" 0 "" "RHEA:42452" "HMR_8565"
61 changes: 9 additions & 52 deletions model/Human-GEM.yml
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Expand Up @@ -11729,14 +11729,6 @@
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00926c"
- name: "4-(2-aminophenyl)-2,4-dioxobutanoate"
- compartment: "c"
- formula: "C10H8NO4"
- charge: -1
- inchis: ""
- metFrom: "HMRdatabase"
- !!omap
- id: "MAM00927c"
- name: "4-(methylnitrosamino)-1-(1-oxido-3-pyridinyl)-1-butanone"
Expand Down Expand Up @@ -81699,41 +81691,6 @@
- subsystem:
- "Tryptophan metabolism"
- confidence_score: 0
- !!omap
- id: "MAR08564"
- name: ""
- metabolites: !!omap
- MAM00926c: 1
- MAM01306c: -1
- MAM01974c: 1
- MAM02319c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000109576 or ENSG00000137944 or ENSG00000171097"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.6.1.7"
- references: ""
- subsystem:
- "Tryptophan metabolism"
- confidence_score: 0
- !!omap
- id: "MAR08565"
- name: ""
- metabolites: !!omap
- MAM00926c: -1
- MAM00990c: 1
- MAM02040c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
- references: ""
- subsystem:
- "Tryptophan metabolism"
- confidence_score: 0
- !!omap
- id: "MAR08566"
- name: ""
Expand Down Expand Up @@ -82834,14 +82791,14 @@
- id: "MAR04222"
- name: ""
- metabolites: !!omap
- MAM00990c: -1
- MAM01306c: 1
- MAM01974c: -1
- MAM02040c: -1
- MAM02319c: 1
- lower_bound: -1000
- MAM00990c: 1
- MAM01306c: -1
- MAM01974c: 1
- MAM02040c: 1
- MAM02319c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000109576 or ENSG00000137944 or ENSG00000171097"
- gene_reaction_rule: "ENSG00000137944 or ENSG00000171097"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.6.1.7"
Expand Down Expand Up @@ -218228,7 +218185,7 @@
- MAM02553m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000159423"
- gene_reaction_rule: "ENSG00000111275 or ENSG00000137124"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.5.1.12"
Expand Down Expand Up @@ -230344,7 +230301,7 @@
- MAM01974m: 1
- MAM02040m: 1
- MAM02319m: -1
- lower_bound: -1000
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000109576 or ENSG00000137944"
- rxnNotes: ""
Expand Down
1 change: 0 additions & 1 deletion model/metabolites.tsv
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Expand Up @@ -1464,7 +1464,6 @@ mets metsNoComp metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMa
"MAM00923c" "MAM00923" "cala" "C02642" "HMDB0000026" "CHEBI:18261" "111" "" "" "HC00975" "cala" "MNXM802" "m00923c" "m00923c"
"MAM00924c" "MAM00924" "42A3HP24DB" "C05645" "" "" "440741" "" "" "HC01547" "42A3HP24DB" "MNXM163203;MNXM4997" "m00924c" "m00924c"
"MAM00925c" "MAM00925" "" "" "" "" "10948689" "" "CE3086" "" "CE3086" "MNXM166294" "m00925c" "m00925c"
"MAM00926c" "MAM00926" "4aphdob" "C01252" "HMDB0000978" "CHEBI:17442" "472" "" "" "" "4aphdob" "MNXM163204" "m00926c" "m00926c"
"MAM00927c" "MAM00927" "" "C19602" "" "" "" "" "" "" "M00927" "MNXM14691" "m00927c" "m00927c"
"MAM00928c" "MAM00928" "" "C19605" "" "" "" "" "" "" "M00928" "MNXM14692" "m00928c" "m00928c"
"MAM00929c" "MAM00929" "" "C19574" "" "" "" "" "" "" "M00929" "MNXM4356" "m00929c" "m00929c"
Expand Down
6 changes: 2 additions & 4 deletions model/reactions.tsv
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Expand Up @@ -748,8 +748,6 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR08091" "" "3HXKYNDCL" "" "" "" "3HXKYNDCL" "MNXR94906" "HMR_8091" "RCR11354" "" 0 "" "" "HMR_8091"
"MAR08092" "R04907" "3HXKYNOXDA" "" "" "" "3HXKYNOXDA" "MNXR94907" "HMR_8092" "RCR11355" "" 0 "" "" "HMR_8092"
"MAR08563" "R02678" "ALDD20xm" "" "" "" "ALDD20xm" "MNXR95744" "HMR_8563" "RCR10320" "" 0 "" "RHEA:30867" "HMR_8563"
"MAR08564" "" "KYNAKGAT" "" "" "" "KYNAKGAT" "MNXR100948" "HMR_8564" "RCR11356" "" 0 "" "" "HMR_8564"
"MAR08565" "R03445" "KYNATESYN" "" "" "" "KYNATESYN" "MNXR100949" "HMR_8565" "RCR11357" "" 0 "" "RHEA:42452" "HMR_8565"
"MAR08566" "" "MELATNOX" "" "" "" "MELATNOX" "MNXR101458" "HMR_8566" "RCR11358" "" 0 "" "" "HMR_8566"
"MAR03935" "R06982" "r1377" "" "r1377" "" "r1377" "MNXR105462;MNXR99239" "HMR_3935" "RCR11359" "" 0 "" "RHEA:22488" "HMR_3935"
"MAR04681" "R00699" "" "" "" "" "PHYCBOXL" "MNXR102650" "HMR_4681" "RCR10321" "" 0 "" "RHEA:19717" "HMR_4681"
Expand Down Expand Up @@ -808,7 +806,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04218" "R03936" "LFORKYNHYD" "R03936C" "r0646" "" "LFORKYNHYD" "MNXR101060;MNXR108539" "HMR_4218" "RCR11391" "" 0 "" "" "HMR_4218"
"MAR04219" "R00988" "" "R00988C" "r0239" "" "r0239" "MNXR105316;MNXR106774" "HMR_4219" "RCR11392" "" 0 "" "" "HMR_4219"
"MAR04220" "R01960" "KYN3OX" "R01960C" "r0455" "" "KYN3OX" "MNXR100947" "HMR_4220" "RCR11393" "" 0 "RHEA:20548" "RHEA:20545" "HMR_4220"
"MAR04222" "" "" "RE1233C" "" "" "RE1233C" "" "HMR_4222" "RCR11394" "" 0 "" "" "HMR_4222"
"MAR04222" "" "" "RE1233C" "" "" "RE1233C" "" "HMR_4222" "RCR11394" "" 0 "RHEA:65561" "RHEA:65560" "HMR_4222;MAR08564+MAR08565"
"MAR04224" "R00987" "KYN" "R00987C" "r0238" "" "KYN" "MNXR100946" "HMR_4224" "RCR11395" "" 0 "" "RHEA:16813" "HMR_4224"
"MAR04225" "R02668" "HKYNH" "R02668C" "r0563" "" "HKYNH" "MNXR100656" "HMR_4225" "RCR10534" "" 0 "" "RHEA:25143" "HMR_4225"
"MAR04227" "R02670" "" "" "" "" "HMR_4227" "MNXR107655" "HMR_4227" "RCR14355" "" 0 "" "" "HMR_4227"
Expand Down Expand Up @@ -8726,7 +8724,7 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR02751" "" "RE1134M" "" "" "" "RE1134M" "MNXR102255" "" "" "" 0 "" "" "RE1134M"
"MAR02756" "" "" "" "" "" "RE1135G" "" "" "" "" 0 "" "" "RE1135G"
"MAR02763" "" "" "" "" "" "RE1135L" "" "" "" "" 0 "" "" "RE1135L"
"MAR02765" "" "" "" "" "" "RE1233M" "" "" "" "" 0 "" "" "RE1233M"
"MAR02765" "" "" "" "" "" "RE1233M" "" "" "" "" 0 "RHEA:65561" "RHEA:65560" "RE1233M"
"MAR02767" "" "RE1309M" "" "" "" "RE1309M" "MNXR103507" "" "" "" 0 "" "" "RE1309M"
"MAR02779" "" "RE1342C" "" "" "" "RE1342C" "MNXR103511" "" "" "" 0 "" "" "RE1342C"
"MAR02781" "" "RE1447M" "" "" "" "RE1447M" "MNXR102717" "" "" "" 0 "" "" "RE1447M"
Expand Down