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fix: rename OG pair file and modify rxn IDs
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- These ids accidentally conflict with recent changes to HumanGEM
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@haowang-bioinfo
haowang-bioinfo committed May 11, 2023
1 parent 142f7b8 commit a4962bf
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Showing 2 changed files with 13 additions and 12 deletions.
3 changes: 2 additions & 1 deletion code/masterScriptMouseGEM.m
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Expand Up @@ -18,7 +18,7 @@
%% Prepare Mouse ortholog pairs and species-specific network

% get ortholog pairs from human to mouse
mouseOrthologPairs = extractAllianceGenomeOrthologs('human2MouseOrthologs.json');
mouseOrthologPairs = extractAllianceGenomeOrthologs('human2MouseOrthologs.tsv');

% load species-specific rxns and mets
rxnsToAdd = importTsvFile('mouseSpecificRxns.tsv');
Expand All @@ -43,6 +43,7 @@
exportTsvFile(metAssoc,'../model/metabolites.tsv');
end

mouseGEM.geneShortNames = mouseGEM.genes;
save('../model/Mouse-GEM.mat', 'mouseGEM');
exportYaml(mouseGEM, '../model/Mouse-GEM.yml');
mouseGEM = annotateGEM(mouseGEM,'../model',{'rxn','met'}); % add annotation data to structure
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22 changes: 11 additions & 11 deletions data/mouseSpecificRxns.tsv
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@@ -1,12 +1,12 @@
rxns equations ub lb eccodes subSystems grRules rxnReferences rxnConfidenceScores rxnKEGGID rxnMetaCycID rxnREACTOMEID rxnMetaNetXID
"MAR20001" "NAD+[m] + threonine[m] => NADH[m] + H+[m] + L-2-amino-3-oxobutanoic acid[m]" 1000 0 "1.1.1.103" "Glycine, serine and threonine metabolism" "Tdh" "PMID:26492815" 4 "R01465" "THREODEHYD-RXN" "R-HSA-6798667" "MNXR103402"
"MAR20002" "N-Acetyllactosamine[g] + UDP-galactose[g] => alpha-D-Galactosyl-1,3-beta-D-galactosyl-1,4-N-acetyl-D-glucosamine[g] + UDP[g] + H+[g]" 1000 0 "2.4.1.87" "Glycosphingolipid biosynthesis" "Ggta1" "" 2 "R04531" "2.4.1.124-RXN" "" "MNXR115091"
"MAR20003" "L-Allothreonine[c] <=> glycine[c] + acetaldehyde[c]" 1000 -1000 "4.1.2.48;4.1.2.49" "Glycine, serine and threonine metabolism" "Tha1" "" 2 "R06171" "LTAA-RXN" "" "MNXR104834"
"MAR20004" "H2O[x] + 5-hydroxyisourate[x] => 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] + H+[x]" 1000 0 "3.5.2.17" "Purine metabolism" "Urah" "PMID:17085964" 4 "R06601" "3.5.2.17-RXN" "" "MNXR100652"
"MAR20005" "5-hydroxyisourate[x] <=> 5-hydroxyisourate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" ""
"MAR20006" "5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] <=> 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" ""
"MAR20007" "2 H2O[x] + O2[x] + 1,3,7-Trimethyluric acid[x] <=> CO2[x] + H2O2[x] + 3,6,8-Trimethylallantoin[x]" 1000 -1000 "1.7.3.3" "Caffeine metabolism" "Uox" "" 2 "R07981" "" "" "MNXR111564"
"MAR20008" "O2[r] + L-gulono-1,4-lactone[r] => H2O2[r] + ascorbate[r] + H+[r]" 1000 0 "1.1.3.8" "Ascorbate and aldarate metabolism" "Gulo" "PMID:14962674" 4 "R10053" "RXN-13689" "" "MNXR116004"
"MAR20009" "O2[r] + L-gulono-1,4-lactone[r] => H2O2[r] + L-xylo-Hexulonolactone[r]" 1000 0 "1.1.3.8" "Ascorbate and aldarate metabolism" "Gulo" "" 2 "R03184" "L-GULONOLACTONE-OXIDASE-RXN" "" "MNXR140097"
"MAR20010" "PAPS[c] + aniline[c] => PAP[c] + Benzenamine sulfate[c] + H+[c]" 1000 0 "2.8.2.3" "Amine sulfotransferase" "Sult3a1" "" 2 "R01861" "" "" "MNXR107208"
"MAR20016" "ascorbate[r] => ascorbate[c]" 1000 0 "" "Transport" "" "" 0 "" "" "" ""
"MAR15001" "NAD+[m] + threonine[m] => NADH[m] + H+[m] + L-2-amino-3-oxobutanoic acid[m]" 1000 0 "1.1.1.103" "Glycine, serine and threonine metabolism" "Tdh" "PMID:26492815" 4 "R01465" "THREODEHYD-RXN" "R-HSA-6798667" "MNXR103402"
"MAR15002" "N-Acetyllactosamine[g] + UDP-galactose[g] => alpha-D-Galactosyl-1,3-beta-D-galactosyl-1,4-N-acetyl-D-glucosamine[g] + UDP[g] + H+[g]" 1000 0 "2.4.1.87" "Glycosphingolipid biosynthesis" "Ggta1" "" 2 "R04531" "2.4.1.124-RXN" "" "MNXR115091"
"MAR15003" "L-Allothreonine[c] <=> glycine[c] + acetaldehyde[c]" 1000 -1000 "4.1.2.48;4.1.2.49" "Glycine, serine and threonine metabolism" "Tha1" "" 2 "R06171" "LTAA-RXN" "" "MNXR104834"
"MAR15004" "H2O[x] + 5-hydroxyisourate[x] => 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] + H+[x]" 1000 0 "3.5.2.17" "Purine metabolism" "Urah" "PMID:17085964" 4 "R06601" "3.5.2.17-RXN" "" "MNXR100652"
"MAR15005" "5-hydroxyisourate[x] <=> 5-hydroxyisourate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" ""
"MAR15006" "5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[x] <=> 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate[c]" 1000 -1000 "" "Transport" "" "" 0 "" "" "" ""
"MAR15007" "2 H2O[x] + O2[x] + 1,3,7-Trimethyluric acid[x] <=> CO2[x] + H2O2[x] + 3,6,8-Trimethylallantoin[x]" 1000 -1000 "1.7.3.3" "Caffeine metabolism" "Uox" "" 2 "R07981" "" "" "MNXR111564"
"MAR15008" "O2[r] + L-gulono-1,4-lactone[r] => H2O2[r] + ascorbate[r] + H+[r]" 1000 0 "1.1.3.8" "Ascorbate and aldarate metabolism" "Gulo" "PMID:14962674" 4 "R10053" "RXN-13689" "" "MNXR116004"
"MAR15009" "O2[r] + L-gulono-1,4-lactone[r] => H2O2[r] + L-xylo-Hexulonolactone[r]" 1000 0 "1.1.3.8" "Ascorbate and aldarate metabolism" "Gulo" "" 2 "R03184" "L-GULONOLACTONE-OXIDASE-RXN" "" "MNXR140097"
"MAR15010" "PAPS[c] + aniline[c] => PAP[c] + Benzenamine sulfate[c] + H+[c]" 1000 0 "2.8.2.3" "Amine sulfotransferase" "Sult3a1" "" 2 "R01861" "" "" "MNXR107208"
"MAR15016" "ascorbate[r] => ascorbate[c]" 1000 0 "" "Transport" "" "" 0 "" "" "" ""

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