Merge pull request #770 from SysBioChalmers/removePeroGenesFromBetaox…

…idationGPRsInMito fix: remove genes only expressed in peroxisome from beta-oxidation reactions in mitochondria
SysBioChalmers · Dec 18, 2023 · 64f32f6 · 64f32f6
2 parents 04a85be + 091f80c
commit 64f32f6
Show file tree

Hide file tree

Showing 2 changed files with 37 additions and 11 deletions.
diff --git a/code/modelCuration/reportPeroxGenesFromBetaoxidationGPRsInMito.py b/code/modelCuration/reportPeroxGenesFromBetaoxidationGPRsInMito.py
@@ -0,0 +1,26 @@
+# 1. read gene compartment from genes.tsv and load model
+# 2. get the reactions in fatty acid oxidation subsystem and mitochondria compartment
+# 3. go through the reactions and check the compartment of each genes in the GPR
+# 4. report the genes that are only expressed in peroxisome
+import csv
+import cobra
+import pandas as pd
+
+# load genes.tsv and read info into a dict for genes and their compartments
+with open("../../model/genes.tsv", 'r') as file:
+    reader = csv.reader(file, delimiter='\t')
+    geneCompDict = {row[0]: row[8] for row in reader}
+
+# load model
+model = cobra.io.load_yaml_model('../../model/Human-GEM.yml')
+
+# collect reactions from "Fatty acid oxidation" subsystem and in [m] compartment
+subsys = 'Fatty acid oxidation'
+targetComp = {'m'}
+for r in model.reactions:
+    if subsys in r.subsystem and targetComp == r.compartments:
+        # go through collected reactions find genes that exist only in peroxisome
+        for g in r.genes:
+            if geneCompDict[g.id] == 'Peroxisome':
+                print(f'{r.id} | {g.id} | {r.build_reaction_string(True)} | {r.gene_reaction_rule} | {r.gene_name_reaction_rule}')
+
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -226667,7 +226667,7 @@
           - MAM02678m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000115425 or ENSG00000116353"
+      - gene_reaction_rule: "ENSG00000116353"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.3.1.38"
@@ -226898,7 +226898,7 @@
           - MAM02644m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000115425 or ENSG00000116353"
+      - gene_reaction_rule: "ENSG00000116353"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.3.1.38"
@@ -226917,7 +226917,7 @@
           - MAM02555m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000115425 or ENSG00000116353"
+      - gene_reaction_rule: "ENSG00000116353"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.3.1.38"
@@ -226936,7 +226936,7 @@
           - MAM02555m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000115425 or ENSG00000116353"
+      - gene_reaction_rule: "ENSG00000116353"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.3.1.38"
@@ -226993,7 +226993,7 @@
           - MAM02555m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000115425 or ENSG00000116353"
+      - gene_reaction_rule: "ENSG00000116353"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.3.1.38"
@@ -227191,7 +227191,7 @@
           - MAM02555m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000115425 or ENSG00000116353"
+      - gene_reaction_rule: "ENSG00000116353"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "1.3.1.38"
@@ -228239,7 +228239,7 @@
           - MAM02677m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000138029 and ENSG00000167315) or (ENSG00000060971 and ENSG00000138029)"
+      - gene_reaction_rule: "ENSG00000138029 or ENSG00000167315"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "2.3.1.86"
@@ -232053,7 +232053,7 @@
           - MAM03334m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000084754 or ENSG00000113790 or ENSG00000127884 or ENSG00000138029"
+      - gene_reaction_rule: "ENSG00000084754 or ENSG00000127884 or ENSG00000138029"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "4.2.1.17"
@@ -232274,7 +232274,7 @@
           - MAM03358m: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000113790 or ENSG00000167969 or ENSG00000198721"
+      - gene_reaction_rule: "ENSG00000167969 or ENSG00000198721"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "5.3.3.8"
@@ -232325,7 +232325,7 @@
           - MAM03361m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000113790 or ENSG00000167969 or ENSG00000198721"
+      - gene_reaction_rule: "ENSG00000167969 or ENSG00000198721"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "5.3.3.8"
@@ -232342,7 +232342,7 @@
           - MAM03361m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000084754 or ENSG00000113790 or ENSG00000127884 or ENSG00000138029"
+      - gene_reaction_rule: "ENSG00000084754 or ENSG00000127884 or ENSG00000138029"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "4.2.1.17"