From ba8a4f3c02e929dda9bd2daa964cc3433318cd65 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:39:41 +0800 Subject: [PATCH] Fix-GPR curation for fatty_acid_oxidation and Glycerolipid_metabolism (#928) * fix: GPR curation for fatty_acid_oxidation and Glycerolipid_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- data/testResults/README.md | 2 +- model/Human-GEM.yml | 24 ++++++++++++------------ 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 5a49a7d3..78746c32 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 #820** (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 #928** (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. ### 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/model/Human-GEM.yml b/model/Human-GEM.yml index 568b3f1d..ca0b3fe0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -131779,7 +131779,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1;1.1.1.2;1.1.1.21;1.1.1.72" @@ -131818,7 +131818,7 @@ - MAM02555m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000085662 or ENSG00000117448 or ENSG00000172955 or ENSG00000187758 or ENSG00000197894 or ENSG00000198074 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1;1.1.1.2;1.1.1.21;1.1.1.72" @@ -134237,7 +134237,7 @@ - MAM02877c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135929" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.1.1.103" @@ -134255,7 +134255,7 @@ - MAM02877c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135929" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.1.1.103" @@ -223471,7 +223471,7 @@ - MAM03727c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "2.3.1.21" @@ -231805,7 +231805,7 @@ - MAM03333m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000161533 or ENSG00000196177" + - gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000196177" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.3.99.3" @@ -232279,7 +232279,7 @@ - MAM02766x: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000068366 or ENSG00000103740 or ENSG00000119673 or ENSG00000123983 or ENSG00000130377 or ENSG00000140284 or ENSG00000151726 or ENSG00000164398 or ENSG00000177465 or ENSG00000197142" + - gene_reaction_rule: "ENSG00000140284" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "6.2.1.3" @@ -237338,7 +237338,7 @@ - MAM03488c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -237917,7 +237917,7 @@ - MAM03496c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -241061,7 +241061,7 @@ - MAM03243c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000110090 or ENSG00000169169 or ENSG00000205560" + - gene_reaction_rule: "ENSG00000110090 or ENSG00000205560" - rxnNotes: "http://www.perkinelmergenetics.com/3Hydroxy3MethylglutarylCoALyaseDeficiency.html" - rxnFrom: "Recon3D" - eccodes: "" @@ -241163,7 +241163,7 @@ - MAM03409x: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000060971 and ENSG00000113790 and ENSG00000133835 and ENSG00000161533" + - gene_reaction_rule: "(ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835) and (ENSG00000060971 or ENSG00000116171)" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -272528,7 +272528,7 @@ - MAM03922x: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000113790 and ENSG00000161533) or (ENSG00000104823 and ENSG00000161533)" + - gene_reaction_rule: "(ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835)" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "1.3.3.6;4.2.1.17"