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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| % This scripts applies curations to be applied on yeast-GEM release 8.6.1. | ||
| % Indicate which Issue/PR are addressed. If multiple curations are performed | ||
| % before a new release is made, just add the required code to this script. If | ||
| % more extensive coding is required, you can write a separate (generic) function | ||
| % that can be kept in the /code/modelCuration folder. Otherwise, try to use | ||
| % existing functions whenever possible. In particular /code/curateMetsRxnsGenes | ||
| % can do many types of curation. | ||
|
|
||
| %% Load yeast-GEM 8.6.1 (requires local yeast-GEM git repository) | ||
| cd .. | ||
| model = getEarlierModelVersion('8.6.1'); | ||
| model.id='yeastGEM_develop'; | ||
| dataDir=fullfile(pwd(),'..','data','modelCuration','v8.6.1'); | ||
| cd modelCuration | ||
|
|
||
| %% Correct ATP synthase mitochondrial complex gene associations (PR #323) | ||
| model = changeGrRules(model, 'r_0226', ['Q0080 and Q0085 and Q0130 and ' ... | ||
| 'YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W ' ... | ||
| 'and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and ' ... | ||
| 'YDR322C-A and YPR020W and YOL077W-A'],true); | ||
| model = deleteUnusedGenes(model); | ||
| checkModelStruct(model,true,false) | ||
|
|
||
| %% DO NOT CHANGE OR REMOVE THE CODE BELOW THIS LINE. | ||
| % Show some metrics: | ||
| cd ../modelTests | ||
| disp('Run gene essentiality analysis') | ||
| [new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model); | ||
| fprintf('Genes in model: %d\n',numel(model.genes)); | ||
| fprintf('Gene essentiality accuracy: %.4f\n', new.accuracy); | ||
| fprintf('True non-essential genes: %d\n', numel(new.tp)); | ||
| fprintf('True essential genes: %d\n', numel(new.tn)); | ||
| fprintf('False non-essential genes: %d\n', numel(new.fp)); | ||
| fprintf('False essential genes: %d\n', numel(new.fn)); | ||
| fprintf('\nRun growth analysis\n') | ||
| R2=growth(model); | ||
| fprintf('R2 of growth prediction: %.4f\n', R2); | ||
|
|
||
| % Save model: | ||
| cd .. | ||
| saveYeastModel(model) | ||
| cd modelCuration |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| MATLAB 9.10.0.1851785 (R2021a) Update 6 | ||
| MATLAB 9.12.0.1956245 (R2022a) Update 2 | ||
| libSBML 5.19.0 | ||
| RAVEN_toolbox commit cef4a35 | ||
| RAVEN_toolbox commit 20950d8 | ||
| COBRA_toolbox unknown |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -3,7 +3,7 @@ | |
| - metaData: | ||
| id: "yeastGEM_develop" | ||
| name: "The Consensus Genome-Scale Metabolic Model of Yeast" | ||
| date: "2022-06-15" | ||
| date: "2022-09-05" | ||
| givenName: "Eduard" | ||
| familyName: "Kerkhoven" | ||
| email: "[email protected]" | ||
|
|
@@ -34954,7 +34954,7 @@ | |
| - s_1326: -1 | ||
| - lower_bound: 0 | ||
| - upper_bound: 1000 | ||
| - gene_reaction_rule: "(Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR322C-A and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W) or (Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YPR020W) or (Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR322C-A and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YJL180C and YLR393W and YNL315C and YOL077W-A and YCL005W-A)" | ||
| - gene_reaction_rule: "Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YDR322C-A and YPR020W and YOL077W-A" | ||
| - eccodes: "3.6.3.14" | ||
| - subsystem: | ||
| - "Oxidative phosphorylation" | ||
|
|
@@ -108261,6 +108261,7 @@ | |
| - name: "YBR241C" | ||
| - !!omap | ||
| - id: "YBR242W" | ||
| - name: "YBR242W" | ||
| - annotation: !!omap | ||
| - kegg.genes: "sce:YBR242W" | ||
| - ncbigene: "852544" | ||
|
|
@@ -109827,9 +109828,6 @@ | |
| - !!omap | ||
| - id: "YJL168C" | ||
| - name: "SET2" | ||
| - !!omap | ||
| - id: "YJL180C" | ||
| - name: "ATP12" | ||
| - !!omap | ||
| - id: "YJL196C" | ||
| - name: "ELO1" | ||
|
|
@@ -110451,9 +110449,6 @@ | |
| - !!omap | ||
| - id: "YLR386W" | ||
| - name: "VAC14" | ||
| - !!omap | ||
| - id: "YLR393W" | ||
| - name: "ATP10" | ||
| - !!omap | ||
| - id: "YLR395C" | ||
| - name: "COX8" | ||
|
|
@@ -110850,9 +110845,6 @@ | |
| - !!omap | ||
| - id: "YNL292W" | ||
| - name: "PUS4" | ||
| - !!omap | ||
| - id: "YNL315C" | ||
| - name: "ATP11" | ||
| - !!omap | ||
| - id: "YNL316C" | ||
| - name: "PHA2" | ||
|
|
@@ -111516,6 +111508,7 @@ | |
| - name: "MET16" | ||
| - !!omap | ||
| - id: "YPR170W-B" | ||
| - name: "YPR170W__45__B" | ||
| - annotation: !!omap | ||
| - kegg.genes: "sce:YPR170W-B" | ||
| - ncbigene: "5848745" | ||
|
|
||