From 8de1c59f7648da0bbcd7feff503dc3d133867355 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Thu, 7 Nov 2024 18:26:47 +0800 Subject: [PATCH 1/2] fix-GPR_curation_for_PPP_TCA_Pyruvate_metabolism --- model/Human-GEM.yml | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e9484f6b..5bc2a52a 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -70005,7 +70005,7 @@ - MAM02819c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000166816 or ENSG00000182224" + - gene_reaction_rule: "ENSG00000166816" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.2.4" @@ -70297,7 +70297,7 @@ - MAM02553c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.1" @@ -70317,7 +70317,7 @@ - MAM02553c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000072210 or ENSG00000108602 or ENSG00000132746 or ENSG00000143149 or ENSG00000164904 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000072210 or ENSG00000108602 or ENSG00000132746 or ENSG00000143149 or ENSG00000164904" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.4;1.2.1.5" @@ -70357,7 +70357,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072210 or ENSG00000111275 or ENSG00000137124 or ENSG00000143149 or ENSG00000164904" + - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000143149 or ENSG00000164904" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.3" @@ -70376,7 +70376,7 @@ - MAM02771c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -70395,7 +70395,7 @@ - MAM02771c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" + - gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000180011 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -70471,7 +70471,7 @@ - MAM02819c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000166816 or ENSG00000182224" + - gene_reaction_rule: "ENSG00000182224" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.2.4" @@ -70488,11 +70488,11 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000148090" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" - - references: "" + - references: "PMID: 25709564" - subsystem: - "Pyruvate metabolism" - confidence_score: 0 @@ -71282,7 +71282,7 @@ - MAM02884c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000067057 or ENSG00000141959 or ENSG00000152556" + - gene_reaction_rule: "ENSG00000067057 or ENSG00000141959" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.11" @@ -71320,7 +71320,7 @@ - MAM03166c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000138030" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.3" @@ -71429,7 +71429,7 @@ - MAM02553r: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000049239 or ENSG00000130313" + - gene_reaction_rule: "ENSG00000049239" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.1.31" @@ -94150,7 +94150,7 @@ - MAM02661x: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000101323 or ENSG00000116882" + - gene_reaction_rule: "ENSG00000101323" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.3.15" @@ -94168,7 +94168,7 @@ - MAM02007x: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000101323 or ENSG00000116882" + - gene_reaction_rule: "ENSG00000101323" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.3.15" @@ -94242,7 +94242,7 @@ - MAM02553c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000006534 or ENSG00000072210 or ENSG00000108602 or ENSG00000132746 or ENSG00000143149 or ENSG00000164904 or ENSG00000184254" + - gene_reaction_rule: "ENSG00000006534 or ENSG00000072210 or ENSG00000108602 or ENSG00000132746 or ENSG00000143149 or ENSG00000164904" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.4;1.2.1.5" @@ -94280,7 +94280,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072210 or ENSG00000111275 or ENSG00000137124 or ENSG00000143149 or ENSG00000164904" + - gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000143149 or ENSG00000164904" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.2.1.3" @@ -302638,7 +302638,7 @@ - MAM02884c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000130957 or ENSG00000165140" + - gene_reaction_rule: "" - rxnNotes: "https://doi.org/10.1007/BF02702726" - rxnFrom: "" - eccodes: "3.1.3.11" From 6de11ff5a16e1544270124ae2ebcaad61b9f518c Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Thu, 7 Nov 2024 10:55:40 +0000 Subject: [PATCH 2/2] 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 160c9df5..5d867bb2 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 #882** (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 #915** (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.