From 5670d60fb7e3a003c3a8eaa53b9f46561ab800a2 Mon Sep 17 00:00:00 2001 From: haowang-bioinfo Date: Wed, 13 Dec 2023 22:57:31 +0100 Subject: [PATCH 1/9] feat: add code to report Perox genes from beta-oxidation GPRs in mito --- ...rtPeroxGenesFromBetaoxidationGPRsInMito.py | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 code/modelCuration/reportPeroxGenesFromBetaoxidationGPRsInMito.py diff --git a/code/modelCuration/reportPeroxGenesFromBetaoxidationGPRsInMito.py b/code/modelCuration/reportPeroxGenesFromBetaoxidationGPRsInMito.py new file mode 100644 index 00000000..20c47843 --- /dev/null +++ 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}') + From 4507ee322489c91a1ad79cef409cc80b82701d53 Mon Sep 17 00:00:00 2001 From: haowang-bioinfo Date: Wed, 13 Dec 2023 23:38:51 +0100 Subject: [PATCH 2/9] fix-GPR: remove ENSG00000115425 from MAR02028 --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e7aec4fe..981d7301 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -226738,7 +226738,7 @@ - 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" From fa7c8140cc5297158b8423d7709b05b339698d8d Mon Sep 17 00:00:00 2001 From: haowang-bioinfo Date: Wed, 13 Dec 2023 23:53:08 +0100 Subject: [PATCH 3/9] fix-GPR: remove ENSG00000115425 from MAR02148 --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 981d7301..757fc5ef 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -226969,7 +226969,7 @@ - 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" From 1c7756295d5566c01cc8d4fc8bc92900167276f8 Mon Sep 17 00:00:00 2001 From: haowang-bioinfo Date: Wed, 13 Dec 2023 23:54:40 +0100 Subject: [PATCH 4/9] fix-GPR: remove ENSG00000115425 from MAR02149 --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 757fc5ef..842b42b9 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -226988,7 +226988,7 @@ - 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" From 1c3360ad75d8ac255c5039b72009d6c4280f0766 Mon Sep 17 00:00:00 2001 From: haowang-bioinfo Date: Wed, 13 Dec 2023 23:58:45 +0100 Subject: [PATCH 5/9] fix-GPR: remove ENSG00000115425 from MAR02187 --- model/Human-GEM.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 842b42b9..196ad332 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -227007,7 +227007,7 @@ - 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" @@ -227064,7 +227064,7 @@ - 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" From f4ba4c9058769d55fc6d86b62ecf253972de857b Mon Sep 17 00:00:00 2001 From: haowang-bioinfo Date: Thu, 14 Dec 2023 00:00:30 +0100 Subject: [PATCH 6/9] fix-GPR: remove ENSG00000115425 from MAR02207 --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 196ad332..ef35c17d 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -227262,7 +227262,7 @@ - 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" From 5e41b87aa73fee89569ef57cbac2f302d85c988e Mon Sep 17 00:00:00 2001 From: haowang-bioinfo Date: Thu, 14 Dec 2023 09:41:30 +0100 Subject: [PATCH 7/9] fix-GPR: remove ENSG00000113790 from GPRs of b-oxidation rxns in mito - remove ENSG00000113790 from GPRs of MAR03297, MAR03374, MAR03378, MAR03379 --- model/Human-GEM.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index ef35c17d..2ab0d7c3 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -232162,7 +232162,7 @@ - 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" @@ -232383,7 +232383,7 @@ - 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" @@ -232434,7 +232434,7 @@ - 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" @@ -232451,7 +232451,7 @@ - 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" From 0be78ee8843665b007742f9f15bc40e29c0f99bf Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sat, 16 Dec 2023 22:36:49 +0100 Subject: [PATCH 8/9] fix-GPR: remove ENSG00000060971 from MAR02381 --- model/Human-GEM.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 2ab0d7c3..552fe93b 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -228310,7 +228310,7 @@ - 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" @@ -232451,7 +232451,7 @@ - MAM03361m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000084754 or ENSG00000127884 or ENSG00000138029" + - gene_reaction_rule: "ENSG00000084754 or +ENSG00000127884 or ENSG00000138029" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "4.2.1.17" From 091f80c18ec6ffd1c22f68f813492bbca494318f Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Sat, 16 Dec 2023 22:38:49 +0100 Subject: [PATCH 9/9] fix: remove accidentally introduced typo --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 552fe93b..20cf65e6 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -232451,7 +232451,7 @@ - MAM03361m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000084754 or +ENSG00000127884 or ENSG00000138029" + - gene_reaction_rule: "ENSG00000084754 or ENSG00000127884 or ENSG00000138029" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "4.2.1.17"