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Fix: GPR curation for Inositol phosphate metabolism #905

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Fix: GPR curation for Inositol phosphate metabolism #905

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bda6caa
fix-GPR_curation_for_Inositol_phosphate_metabolism
JHL-452b Nov 5, 2024
8a5cedd
chore: add macaw test result
JHL-452b Nov 5, 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 #905** (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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18 changes: 9 additions & 9 deletions model/Human-GEM.yml
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Expand Up @@ -150543,7 +150543,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000104331 or ENSG00000133731 or ENSG00000141401"
- gene_reaction_rule: "ENSG00000133731 or ENSG00000141401"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.25"
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- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163082 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000198881 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920"
- gene_reaction_rule: "ENSG00000003987 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000198881 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.-"
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- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163082 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920"
- gene_reaction_rule: "ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000211456"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.-"
Expand Down Expand Up @@ -150838,7 +150838,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163082 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000198881 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920"
- gene_reaction_rule: "ENSG00000003987 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000165458 or ENSG00000198825 or ENSG00000198881 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.-"
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- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000104331 or ENSG00000133731 or ENSG00000141401"
- gene_reaction_rule: "ENSG00000133731 or ENSG00000141401"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.25"
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- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000104331 or ENSG00000133731 or ENSG00000141401"
- gene_reaction_rule: "ENSG00000133731 or ENSG00000141401"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.25"
Expand Down Expand Up @@ -151373,7 +151373,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000126821 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000144048 or ENSG00000163082 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920"
- gene_reaction_rule: "ENSG00000003987 or ENSG00000054148 or ENSG00000063601 or ENSG00000087053 or ENSG00000102043 or ENSG00000111077 or ENSG00000111696 or ENSG00000112367 or ENSG00000125458 or ENSG00000137770 or ENSG00000139304 or ENSG00000139505 or ENSG00000163719 or ENSG00000165458 or ENSG00000165688 or ENSG00000198825 or ENSG00000205309 or ENSG00000205808 or ENSG00000211456 or ENSG00000213920"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.-"
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- MAM02735c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000107242 or ENSG00000143398 or ENSG00000167103 or ENSG00000186111"
- gene_reaction_rule: "ENSG00000143398 or ENSG00000167103 or ENSG00000186111"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.1.68"
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- MAM02734n: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000107242 or ENSG00000143398 or ENSG00000167103 or ENSG00000186111"
- gene_reaction_rule: "ENSG00000107242 or ENSG00000143398 or ENSG00000167103"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: ""
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