From 0c64152221c698b3a32a45657e347b264473ec33 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 23 Dec 2024 11:05:06 -0500 Subject: [PATCH 1/4] fix: remove peroxisomal genes from mitochondrial acyl-CoA dehydrogenase reactions --- model/Human-GEM.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 8e34d936..ca784ee9 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -62692,7 +62692,7 @@ - MAM02774m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971 or ENSG00000151498 or ENSG00000177646 or ENSG00000196177 or ENSG00000240303" + - gene_reaction_rule: "ENSG00000122971 or ENSG00000151498 or ENSG00000196177" - rxnFrom: "HMRdatabase" - eccodes: - "1.3.99.3" @@ -63045,7 +63045,7 @@ - MAM01803m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117054 or ENSG00000122971 or ENSG00000151498 or ENSG00000177646 or ENSG00000196177 or ENSG00000240303" + - gene_reaction_rule: "ENSG00000122971 or ENSG00000151498 or ENSG00000196177" - rxnFrom: "HMRdatabase" - eccodes: "1.3.99.3" - references: "PMID:13295225;PMID:3597357" @@ -96078,7 +96078,7 @@ - MAM02630m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000087008 or ENSG00000161533" + - gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000177646" - rxnFrom: "HMRdatabase" - eccodes: "1.3.3.6" - references: "PMID:12054595" @@ -96318,7 +96318,7 @@ - MAM02630m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000087008 or ENSG00000161533" + - gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000177646" - rxnFrom: "HMRdatabase" - eccodes: "1.3.3.6" - references: "PMID:11368003;PMID:9862787" @@ -200344,7 +200344,7 @@ - MAM03333m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000196177" + - gene_reaction_rule: "ENSG00000115361" - rxnFrom: "Recon3D" - eccodes: "1.3.99.3" - references: "PMID:1047780;PMID:11135616;PMID:8973539" @@ -203468,7 +203468,7 @@ - MAM03352m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000161533" + - gene_reaction_rule: "ENSG00000072778 or ENSG00000115361" - rxnFrom: "Recon3D" - eccodes: "1.3.3.6" - references: "PMID:11356164;PMID:7775433" From 61f560c28368dd6acb527500c7166e67daeba631 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 23 Dec 2024 16:12:52 +0000 Subject: [PATCH 2/4] chore: add macaw test result --- data/testResults/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 24c52291..578e4af3 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -4,7 +4,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/ The test results shown here were obtained by the GitHub Actions run in: -- **PR #830** (MACAW) +- **PR #943** (MACAW) - **PR #883** (gene essentiality) The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request. From 6f98208ce5f48feb57193741b44a91356851e339 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Mon, 23 Dec 2024 11:37:58 -0500 Subject: [PATCH 3/4] fix: adds ACAD11 to GPRs of MAR03107 and MAR03111 to ensure it is still associated with reactions --- model/Human-GEM.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index ca784ee9..fe0fad17 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -105180,13 +105180,14 @@ - MAM01803m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646" + - gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646 or ENSG00000240303" - rxnFrom: "HMRdatabase" - eccodes: - "1.3.8.7" - "1.3.8.8" - "1.3.8.9" - "1.3.99.-" + - references: "PMID:21237683" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 @@ -105248,13 +105249,14 @@ - MAM01803m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646" + - gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646 or ENSG00000240303" - rxnFrom: "HMRdatabase" - eccodes: - "1.3.8.7" - "1.3.8.8" - "1.3.8.9" - "1.3.99.-" + - references: "PMID:21237683" - subsystem: - "Beta oxidation of even-chain fatty acids (mitochondrial)" - confidence_score: 0 From dca568302c3a70465cf419294dc95c44332a3482 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Tue, 24 Dec 2024 04:46:16 +0100 Subject: [PATCH 4/4] chore: add gene essentiality test result --- data/testResults/README.md | 2 +- data/testResults/gene-essential.csv | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 578e4af3..47ffe8d8 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -5,7 +5,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/ The test results shown here were obtained by the GitHub Actions run in: - **PR #943** (MACAW) -- **PR #883** (gene essentiality) +- **PR #943** (gene essentiality) The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request. diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv index 90a498c1..c918efe0 100644 --- a/data/testResults/gene-essential.csv +++ b/data/testResults/gene-essential.csv @@ -1,7 +1,7 @@ cellLine,TP,TN,FP,FN,accuracy,sensitivity,specificity,F1,MCC -DLD1,37,2165,62,277,0.8666,0.1178,0.9722,0.1792,0.1531 -GBM,34,2147,65,294,0.8587,0.1037,0.9706,0.1593,0.1287 -HCT116,46,2189,57,305,0.8606,0.1311,0.9746,0.2026,0.1851 -HELA,31,2246,72,249,0.8764,0.1107,0.9689,0.1619,0.1266 -RPE1,15,2186,84,255,0.8665,0.05556,0.963,0.0813,0.02954 -all,7,2386,96,109,0.9211,0.06034,0.9613,0.06393,0.02293 +DLD1,50,2147,85,272,0.8602,0.1553,0.9619,0.2188,0.1739 +GBM,57,2138,78,280,0.8598,0.1691,0.9648,0.2415,0.2026 +HCT116,71,2179,70,289,0.8624,0.1972,0.9689,0.2834,0.2534 +HELA,35,2219,106,251,0.8633,0.1224,0.9544,0.1639,0.1061 +RPE1,21,2163,114,255,0.8555,0.07609,0.9499,0.1022,0.0361 +all,8,2357,133,113,0.9058,0.06612,0.9466,0.06107,0.01181