Merge pull request #429 from SysBioChalmers/feat/addACOD1

feat: add cis-aconitate decarboxylase reaction and change reversibility for MAR09498
SysBioChalmers · Nov 10, 2022 · e2fff54 · e2fff54
2 parents b500274 + 5dc9498
commit e2fff54
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Showing 5 changed files with 60 additions and 3 deletions.
diff --git a/code/modelCuration/addRxnACOD1_20221102.m b/code/modelCuration/addRxnACOD1_20221102.m
@@ -0,0 +1,33 @@
+% load model and new reaction info
+ihuman = importYaml('../../model/Human-GEM.yml');
+rxnsToAdd = importTsvFile('../../data/modelCuration/addRxnACOD1_20221102.tsv');
+
+% add new genes to Human-GEM
+newGEM = ihuman;
+newGEM.genes = [newGEM.genes; rxnsToAdd.grRules];
+newGEM.rxnGeneMat(:, end+1) = 0;
+
+% reformat subsystem 
+if ~iscell(rxnsToAdd.subSystems{1})
+    rxnsToAdd.subSystems = cellfun(@(s) {{s}}, rxnsToAdd.subSystems);
+end
+% add new reaction
+newGEM = addRxns(newGEM, rxnsToAdd, 3);
+
+% add reaction annotation
+rxnAssoc = importTsvFile('../../model/reactions.tsv');
+annoNames = fieldnames(rxnAssoc);
+for i=1:length(annoNames)
+    if ismember(annoNames{i}, fieldnames(rxnsToAdd))
+        rxnAssoc.(annoNames{i}) = [rxnAssoc.(annoNames{i}); rxnsToAdd.(annoNames{i})];
+    elseif isequal(annoNames{i},'spontaneous')
+        rxnAssoc.(annoNames{i}) = [rxnAssoc.(annoNames{i}); 0];
+    else
+        rxnAssoc.(annoNames{i}) = [rxnAssoc.(annoNames{i}); {''}];
+    end
+end
+
+% update yaml model and reaction association file
+exportYaml(newGEM, '../../model/Human-GEM.yml');
+exportTsvFile(rxnAssoc,'../../model/reactions.tsv');
+
diff --git a/data/modelCuration/addRxnACOD1_20221102.tsv b/data/modelCuration/addRxnACOD1_20221102.tsv
@@ -0,0 +1,2 @@
+rxns	equations	ub	lb	eccodes	subSystems	grRules	rxnReferences	rxnConfidenceScores	rxnKEGGID	rxnMetaCycID	rxnMetaNetXID	rxnRheaID	rxnRheaMasterID
+"MAR13087"	"cis-aconitate[m] + H+[m] => CO2[m] + itaconate[m]"	1000	0	"4.1.1.6"	"C5-branched dibasic acid metabolism"	"ENSG00000102794"	"PMID:23610393;PMID:31548418"	4	"R02243"	"ACONITATE-DECARBOXYLASE-RXN"	"MNXR107402"	"RHEA:15254"	"RHEA:15253"
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -4,7 +4,7 @@
     short_name: "Human-GEM"
     full_name: "Generic genome-scale metabolic model of Homo sapiens"
     version: ""
-    date: "2022-07-27"
+    date: "2022-11-09"
     authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas"
     email: "[email protected]"
     organization: "Chalmers University of Technology"
@@ -163029,13 +163029,13 @@
           - MAM00216c: 1
           - MAM01719c: -1
           - MAM01720c: 1
-      - lower_bound: -1000
+      - lower_bound: 0
       - upper_bound: 1000
       - gene_reaction_rule: "ENSG00000170430"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.1.1.63"
-      - references: ""
+      - references: "PMID:34982531"
       - subsystem:
           - "Isolated"
       - confidence_score: 0
@@ -305064,6 +305064,24 @@
       - subsystem:
           - "Transport reactions"
       - confidence_score: 2
+    - !!omap
+      - id: "MAR13087"
+      - name: ""
+      - metabolites: !!omap
+          - MAM01580m: -1
+          - MAM01596m: 1
+          - MAM02039m: -1
+          - MAM02191m: 1
+      - lower_bound: 0
+      - upper_bound: 1000
+      - gene_reaction_rule: "ENSG00000102794"
+      - rxnNotes: ""
+      - rxnFrom: ""
+      - eccodes: "4.1.1.6"
+      - references: "PMID:23610393;PMID:31548418"
+      - subsystem:
+          - "C5-branched dibasic acid metabolism"
+      - confidence_score: 4
 - genes:
     - !!omap
       - id: "ENSG00000000419"
@@ -311199,6 +311217,8 @@
       - id: "ENSG00000288702"
     - !!omap
       - id: "ENSG00000288705"
+    - !!omap
+      - id: "ENSG00000102794"
 - compartments: !!omap
     - e: "Extracellular"
     - x: "Peroxisome"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -3066,3 +3066,4 @@ genes	geneENSTID	geneENSPID	geneUniProtID	geneSymbols	geneEntrezID	geneNames	gen
 "ENSG00000285269"	"ENST00000464104;ENST00000463517;ENST00000643789"	"ENSP00000494818"	""	""	"11046"	"novel transcript, SLC35D2-HSD17B3 readthrough"	""
 "ENSG00000288702"	"ENST00000482026"	"ENSP00000418532"	"P35503"	"UGT1A3"	"54659"	"UDP glucuronosyltransferase family 1 member A3"	"UGT1C"
 "ENSG00000288705"	"ENST00000373414"	"ENSP00000362513"	"P35504"	"UGT1A5"	"54579"	"UDP glucuronosyltransferase family 1 member A5"	"UGT1E"
+"ENSG00000102794"	"ENST00000377462;ENST00000449753"	"ENSP00000366682;ENSP00000401584"	"A6NK06"	"ACOD1"	"730249"	"aconitate decarboxylase 1"	"CAD;IRG1"
diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -13025,3 +13025,4 @@ rxns	rxnKEGGID	rxnBiGGID	rxnEHMNID	rxnHepatoNET1ID	rxnREACTOMEID	rxnRecon3DID	rx
 "MAR13084"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
 "MAR13085"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
 "MAR13086"	""	""	""	""	""	""	""	""	""	""	0	""	""	""
+"MAR13087"	"R02243"	""	""	""	""	""	"MNXR107402"	""	""	""	0	"RHEA:15254"	"RHEA:15253"	""
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		rxns equations ub lb eccodes subSystems grRules rxnReferences rxnConfidenceScores rxnKEGGID rxnMetaCycID rxnMetaNetXID rxnRheaID rxnRheaMasterID
		"MAR13087" "cis-aconitate[m] + H+[m] => CO2[m] + itaconate[m]" 1000 0 "4.1.1.6" "C5-branched dibasic acid metabolism" "ENSG00000102794" "PMID:23610393;PMID:31548418" 4 "R02243" "ACONITATE-DECARBOXYLASE-RXN" "MNXR107402" "RHEA:15254" "RHEA:15253"