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Fix: GPR curation for Sulfur metabolism #937

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merged 2 commits into from
Dec 16, 2024
Merged

Fix: GPR curation for Sulfur metabolism #937

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de49640
Fix: GPR curation for Sulfur metabolism
JHL-452b Dec 7, 2024
05cd3f4
chore: add macaw test result
JHL-452b Dec 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 #913** (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 #937** (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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- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000104331 or ENSG00000162813"
- gene_reaction_rule: "ENSG00000162813"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.7"
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- MAM02877c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
- gene_reaction_rule: "ENSG00000006534 or ENSG00000132746 or ENSG00000184254"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.1.5"
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- MAM02946l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000049860 or ENSG00000068001 or ENSG00000106302 or ENSG00000106304 or ENSG00000114378 or ENSG00000169660 or ENSG00000186792 or ENSG00000213614"
- gene_reaction_rule: "ENSG00000049860 or ENSG00000068001 or ENSG00000106302 or ENSG00000114378 or ENSG00000169660 or ENSG00000186792 or ENSG00000213614"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.2.1.35;3.2.1.52"
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- MAM02946l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
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- MAM02946l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
Expand Down Expand Up @@ -140508,7 +140508,7 @@
- MAM02946l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
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- MAM02946l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
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- MAM02946l: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386"
- gene_reaction_rule: "ENSG00000064601 and ENSG00000141012 and ENSG00000170266"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.6.4;3.2.1.18;3.2.1.23;3.4.16.5"
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- MAM02682g: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196"
- gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.8.2.-"
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