fix: rename OG pair file and modify rxn IDs

- These ids accidentally conflict with recent changes to HumanGEM

Author: haowang-bioinfo

code/masterScriptMouseGEM.m

@@ -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');
@@ -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

data/mouseSpecificRxns.tsv

@@ -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	""	""	""	""