From 5af417378888f0c62c72760fd51934631c5b797e Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 09:03:03 +0800 Subject: [PATCH] Fix: GPR curation for Androgen metabolism and Prostaglandin biosynthesis (#935) * Fix: GPR curation for Androgen metabolism and Prostaglandin biosynthesis * chore: add macaw test result * chore: add gene essentiality test result --------- Co-authored-by: JHL-452b Co-authored-by: feiranl <32157802+feiranl@users.noreply.github.com> Co-authored-by: feiranl Co-authored-by: Eduard Kerkhoven --- data/testResults/README.md | 2 +- data/testResults/gene-essential.csv | 12 ++++++------ model/Human-GEM.yml | 14 +++++++------- 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 3ed4bf13..69d9e1fb 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -2,7 +2,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset. -The test results shown here were obtained by the GitHub Actions run in **PR #907** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. +The test results shown here were obtained by the GitHub Actions run in **PR #935** (MACAW) and **PR #935** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR. ### MACAW: `dead_end_test` Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in. diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv index 7a3cef63..19c3e07a 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 -DLD1,36,2185,59,279,0.8679,0.1143,0.9737,0.1756,0.1529 -GBM,34,2165,61,298,0.8597,0.1024,0.9726,0.1593,0.1333 -HCT116,46,2207,53,309,0.8616,0.1296,0.9765,0.2026,0.1905 -HELA,30,2263,69,254,0.8765,0.1056,0.9704,0.1567,0.124 -RPE1,14,2204,81,259,0.8671,0.05128,0.9646,0.07609,0.02585 -all,7,2408,92,109,0.9232,0.06034,0.9632,0.06512,0.0254 +DLD1,36,2183,59,279,0.8678,0.1143,0.9737,0.1756,0.1529 +GBM,34,2163,61,298,0.8595,0.1024,0.9726,0.1593,0.1333 +HCT116,46,2205,53,309,0.8615,0.1296,0.9765,0.2026,0.1904 +HELA,30,2262,69,253,0.8768,0.106,0.9704,0.1571,0.1244 +RPE1,14,2202,81,259,0.867,0.05128,0.9645,0.07609,0.0258 +all,7,2406,92,109,0.9231,0.06034,0.9632,0.06512,0.02537 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index f2c8da17..51d5ea87 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -123722,7 +123722,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000148795 or ENSG00000197580" + - gene_reaction_rule: "ENSG00000148795" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.14.99.-" @@ -123743,7 +123743,7 @@ - MAM02630r: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000148795 or ENSG00000197580" + - gene_reaction_rule: "ENSG00000148795" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.14.99.-" @@ -123895,7 +123895,7 @@ - MAM02969c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000025423 or ENSG00000086696 or ENSG00000108786 or ENSG00000130948 or ENSG00000132196 or ENSG00000149084 or ENSG00000196139 or ENSG00000198189 or ENSG00000204228" + - gene_reaction_rule: "ENSG00000025423 or ENSG00000086696 or ENSG00000108786 or ENSG00000130948 or ENSG00000132196 or ENSG00000196139 or ENSG00000198189 or ENSG00000204228" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.62;1.1.1.64" @@ -123914,7 +123914,7 @@ - MAM02969r: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000025423 or ENSG00000086696 or ENSG00000108786 or ENSG00000130948 or ENSG00000132196 or ENSG00000149084 or ENSG00000196139 or ENSG00000198189 or ENSG00000204228" + - gene_reaction_rule: "ENSG00000025423 or ENSG00000108786 or ENSG00000130948 or ENSG00000132196 or ENSG00000149084 or ENSG00000196139 or ENSG00000198189" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.62;1.1.1.64" @@ -137858,7 +137858,7 @@ - MAM02786c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000163684 or ENSG00000244486" + - gene_reaction_rule: "ENSG00000244486" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.-" @@ -137926,7 +137926,7 @@ - MAM02794c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000196139" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.188" @@ -138855,7 +138855,7 @@ - MAM02785c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000163684 or ENSG00000244486" + - gene_reaction_rule: "ENSG00000244486" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "4.2.1.-"