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fix-GPR curation for PPP, TCA and Pyruvate metabolism #915

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fix-GPR curation for PPP, TCA and Pyruvate metabolism #915

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8de1c59
fix-GPR_curation_for_PPP_TCA_Pyruvate_metabolism
JHL-452b Nov 7, 2024
6de11ff
chore: add macaw test result
JHL-452b Nov 7, 2024
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2 changes: 1 addition & 1 deletion data/testResults/README.md
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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.
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34 changes: 17 additions & 17 deletions model/Human-GEM.yml
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Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand Down Expand Up @@ -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"
Expand All @@ -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: ""
Expand All @@ -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: ""
Expand Down Expand Up @@ -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"
Expand All @@ -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
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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"
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