Add transport rxn GPR

ComplementaryData/modelCuration/TransRxnNewGPR.tsv

@@ -0,0 +1,102 @@
+rxnID	new_gpr
+r_4468	( YDR342C or YHR092C )
+r_1735	YBL042C
+r_4493	YNL065W
+r_4387	( YJR152W or YKR093W )
+r_4398	( YJR152W or YKR093W )
+r_4408	( YJR152W or YKR093W )
+r_4473	( YJR152W or YKR093W )
+r_4429	( YJR152W or YKR093W )
+r_4471	( YJR152W or YKR093W )
+r_4402	( YJR152W or YKR093W )
+r_2190	YNL065W
+r_1707	( YDR342C or YHR092C )
+r_1717	( YDL245C or YEL069C or YJR158W or YNR072W )
+r_2041	( YDR342C or YHR092C )
+r_4395	( YDL245C or YDR342C or YDR343C or YDR345C or YEL069C or YFL011W or YHR092C or YHR094C or YHR096C or YJL214W or YJL219W or YJR158W or YMR011W or YNR072W or YOL156W )
+r_1719	YHR092C
+r_1149	YGL077C
+r_1795	YNL065W
+r_1990	YJL212C
+r_4404	( YJR152W or YKR093W )
+r_4424	( YJR152W or YKR093W )
+r_4437	( YJR152W or YKR093W )
+r_4361	( YJR152W or YKR093W )
+r_1816	YNL065W
+r_2191	YNL065W
+r_1877	( YDR342C or YHR092C )
+r_4469	YKR039W
+r_1908	( YDL245C or YEL069C or YJR158W or YNR072W )
+r_1910	( YDL245C or YDR342C or YDR343C or YDR345C or YEL069C or YFL011W or YHR092C or YHR094C or YHR096C or YJL214W or YJL219W or YJR158W or YMR011W or YNR072W or YOL156W )
+r_4448	( YJR152W or YKR093W )
+r_4457	YDR093W
+r_2040	YOR306C
+r_2105	( YDL245C or YLL043W )
+r_1882	YOR100C
+r_3607	YCR098C
+r_1574	YKL120W
+r_1642	YPR011C
+r_1684	( YGL077C or YOR161C )
+r_3959	YBR192W
+r_3680	YHR002W
+r_3960	YBR192W
+r_1760	( YIL013C or YOR011W )
+r_1803	YGL225W
+r_2094	( YLL052C or YPR192W )
+r_3526	( YLL052C or YPR192W )
+r_3604	( YLL052C or YLL053C or YPR192W )
+r_1179	( YJL133W or YKR052C )
+r_1657	YBR147W
+r_1658	YDR508C
+r_1811	YPR058W
+r_1837	YBR147W
+r_1919	YBR147W
+r_1935	YDR508C
+r_1907	YKR039W
+r_2045	YDR508C
+r_3545	YKR039W
+r_2072	YDR508C
+r_1771	( YKL188C and YPL147W )
+r_1772	( YKL188C and YPL147W )
+r_1976	YOR100C
+r_2231	( YKL188C and YPL147W )
+r_1774	( YKL188C and YPL147W )
+r_3961	( YER053C or YJR077C or YLR348C )
+r_2008	YNR013C
+r_3605	( YCR037C or YJL198W or YML123C )
+r_3649	YNR013C
+r_3893	YIL048W
+r_3813	( YIL048W or YMR162C )
+r_3897	YIL048W
+r_3817	( YIL048W or YMR162C )
+r_3894	YIL048W
+r_3814	( YIL048W or YMR162C )
+r_3898	YIL048W
+r_3818	( YIL048W or YMR162C )
+r_3895	YIL048W
+r_3815	( YIL048W or YMR162C )
+r_3899	YIL048W
+r_3819	( YIL048W or YMR162C )
+r_3896	YIL048W
+r_3816	( YIL048W or YMR162C )
+r_3900	YIL048W
+r_3820	( YIL048W or YMR162C )
+r_3821	YAL026C
+r_3885	YAL026C
+r_3825	YAL026C
+r_3889	YAL026C
+r_3822	YAL026C
+r_3886	YAL026C
+r_3826	YAL026C
+r_3890	YAL026C
+r_3823	YAL026C
+r_3887	YAL026C
+r_3827	YAL026C
+r_3891	YAL026C
+r_3824	YAL026C
+r_3888	YAL026C
+r_3828	YAL026C
+r_3892	YAL026C
+r_3606	YCR098C
+r_1236	( YKL188C and YPL147W )
+r_2107	( YIL013C or YOR011W )

ComplementaryScripts/modelCuration/addTransNewGPR.m

@@ -0,0 +1,51 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% addTransNewGPR
+% Add changes from the database new anootation for new genes + manual curation on those changes
+% Input: model, databasenewGPR.tsv,SGDgeneNames.tsv.
+% As for the reference of new GPR, please find detailed information in:
+% ComplementaryData/databases/DBnewGeneAnnotation.tsv
+% NOTE: changeGeneAssociation.m is a function from cobra
+%
+% Feiran Li & Hongzhong Lu
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Load model
+cd ..
+model = loadYeastModel;
+
+% Change GPR relations
+fid           = fopen('../ComplementaryData/modelCuration/TransRxnNewGPR.tsv');
+changegpr     = textscan(fid,'%s %s','Delimiter','\t','HeaderLines',1);
+newGPR.ID     = changegpr{1};
+newGPR.GPR    = changegpr{2};
+fclose(fid);
+for i = 1:length(newGPR.ID)
+    rxnIndex = find(strcmp(model.rxns, newGPR.ID(i)));
+    model    = changeGeneAssociation(model, model.rxns{rxnIndex}, newGPR.GPR{i});
+end
+
+% Delete unused genes (if any)
+model = removeUnusedGenes(model);
+
+% Add gene standard name for new genes
+fid = fopen('../ComplementaryData/databases/SGDgeneNames.tsv');
+yeast_gene_annotation = textscan(fid,'%s %s','Delimiter','\t','HeaderLines',1);
+fclose(fid);
+for i = 1: length(model.genes)
+    geneIndex = strcmp(yeast_gene_annotation{1}, model.genes{i});
+    if sum(geneIndex) == 1 && ~isempty(yeast_gene_annotation{2}{geneIndex})
+        model.geneNames{i} = yeast_gene_annotation{2}{geneIndex};
+    else
+        model.geneNames{i} = model.genes{i};
+    end
+end
+
+% Add protein name for genes
+for i = 1:length(model.genes)
+    model.proteins{i} = strcat('COBRAProtein',num2str(i));
+end
+
+% Save model:
+model = rmfield(model,'grRules');
+saveYeastModel(model)
+cd modelCuration

ModelFiles/dependencies.txt

@@ -1,7 +1,7 @@
 MATLAB	9.1.0.441655 (R2016b)
 libSBML	5.17.0
-RAVEN_toolbox	2.0.4
-COBRA_toolbox	commit 74dc79a
+RAVEN_toolbox	2.1.0
+COBRA_toolbox	3.0.2
 SBML_level	3
 SBML_version	1
 fbc_version	2