Merge pull request #186 from SysBioChalmers/correct-gene-rule

fix-correct a gene name for one rxn
SysBioChalmers · May 3, 2019 · 43dd80e · 43dd80e
2 parents e0b6846 + 37a5569
commit 43dd80e
Show file tree

Hide file tree

Showing 5 changed files with 7 additions and 11 deletions.
diff --git a/ModelFiles/dependencies.txt b/ModelFiles/dependencies.txt
@@ -1,7 +1,7 @@
 MATLAB	9.1.0.441655 (R2016b)
 libSBML	5.17.0
 RAVEN_toolbox	2.1.0
-COBRA_toolbox	3.0.3
+COBRA_toolbox	3.0.4
 SBML_level	3
 SBML_version	1
 fbc_version	2
diff --git a/ModelFiles/txt/yeastGEM.txt b/ModelFiles/txt/yeastGEM.txt
@@ -3953,7 +3953,7 @@ r_4588	s_4200[e]  <=> s_3778[c] 	YNL275W	-1000.00	1000.00	  0.00
 r_4589	s_0796[e] + s_4201[e]  <=> s_0794[c] + s_4019[c] 	YOL122C	-1000.00	1000.00	  0.00
 r_4590	s_0796[e] + s_4202[e]  <=> s_0794[c] + s_3801[c] 	YGR191W	-1000.00	1000.00	  0.00
 r_4591	s_0796[e] + s_4203[e]  <=> s_0794[c] + s_3822[c] 	( YGL255W or YLR130C )	-1000.00	1000.00	  0.00
-r_4592	s_0796[e] + s_4204[e]  <=> s_0794[c] + s_4013[c] 	( GR191W or YOL130W )	-1000.00	1000.00	  0.00
+r_4592	s_0796[e] + s_4204[e]  <=> s_0794[c] + s_4013[c] 	( YGR191W or YOL130W )	-1000.00	1000.00	  0.00
 r_4593	s_4200[e]  <=> 		-1000.00	1000.00	  0.00
 r_4594	s_4201[e]  <=> 		-1000.00	1000.00	  0.00
 r_4595	s_4202[e]  <=> 		-1000.00	1000.00	  0.00

diff --git a/ModelFiles/xml/yeastGEM.xml b/ModelFiles/xml/yeastGEM.xml
@@ -192749,7 +192749,7 @@
           <speciesReference species="s_4193__91__c__93__" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="r_4587" sboTerm="SBO:0000655" id="r_4587" name="Ca(2+) transport " reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
+      <reaction metaid="r_4587" sboTerm="SBO:0000655" id="r_4587" name="Ca(2+) transport" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
         <notes>
           <body xmlns="http://www.w3.org/1999/xhtml">
             <p>Confidence Level: 2</p>
@@ -192958,7 +192958,7 @@
         </listOfProducts>
         <fbc:geneProductAssociation>
           <fbc:or>
-            <fbc:geneProductRef fbc:geneProduct="G_GR191W"/>
+            <fbc:geneProductRef fbc:geneProduct="G_YGR191W"/>
             <fbc:geneProductRef fbc:geneProduct="G_YOL130W"/>
           </fbc:or>
         </fbc:geneProductAssociation>
@@ -194309,7 +194309,6 @@
       <fbc:geneProduct metaid="G_YNL275W" fbc:id="G_YNL275W" fbc:name="COBRAProtein1135" fbc:label="BOR1"/>
       <fbc:geneProduct metaid="G_YGL255W" fbc:id="G_YGL255W" fbc:name="COBRAProtein1136" fbc:label="ZRT1"/>
       <fbc:geneProduct metaid="G_YLR130C" fbc:id="G_YLR130C" fbc:name="COBRAProtein1137" fbc:label="ZRT2"/>
-      <fbc:geneProduct metaid="G_GR191W" fbc:id="G_GR191W" fbc:name="COBRAProtein1138" fbc:label="GR191W"/>
       <fbc:geneProduct metaid="G_YOL130W" fbc:id="G_YOL130W" fbc:name="COBRAProtein1139" fbc:label="ALR1"/>
       <fbc:geneProduct metaid="G_YNL065W" fbc:id="G_YNL065W" fbc:name="COBRAProtein1140" fbc:label="AQR1"/>
       <fbc:geneProduct metaid="G_YKR093W" fbc:id="G_YKR093W" fbc:name="COBRAProtein1141" fbc:label="PTR2"/>

diff --git a/ModelFiles/yml/yeastGEM.yml b/ModelFiles/yml/yeastGEM.yml
@@ -94018,7 +94018,7 @@
       - s_4204: -1
     - lower_bound: -1000
     - upper_bound: 1000
-    - gene_reaction_rule: GR191W or YOL130W
+    - gene_reaction_rule: YGR191W or YOL130W
     - annotation: !!omap
       - metanetx.reaction: MNXR101553
       - sbo: SBO:0000655
@@ -94118,9 +94118,6 @@
     - annotation: !!omap
       - sbo: SBO:0000627
 - genes:
-  - !!omap
-    - id: GR191W
-    - name: GR191W
   - !!omap
     - id: Q0045
     - name: COX1

diff --git a/README.md b/README.md
@@ -10,13 +10,13 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 **GEM Category:** species; **Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** reconstruction, curated; **Model Source:** YeastMetabolicNetwork; **Omic Source:** genomics, metabolomics; **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** general metabolism; **Bioreactor**; **Strain:** S288C; **Condition:** aerobic, glucose-limited, defined media;
 
-* Last update: 2018-12-06
+* Last update: 2019-02-06
 
 * Main Model Descriptors:
 
 |Taxonomy | Template Model | Reactions | Metabolites| Genes |
 |:-------:|:--------------:|:---------:|:----------:|:-----:|
-|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3963|2691|1150|
+|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3963|2691|1149|
 
 This repository is administered by Benjamín J. Sánchez ([@BenjaSanchez](https://github.com/benjasanchez)), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.