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Fix-GPR curation for fatty_acid_oxidation and Glycerolipid_metabolism #928

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merged 3 commits into from
Dec 17, 2024
Merged

Fix-GPR curation for fatty_acid_oxidation and Glycerolipid_metabolism #928

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6f61b24
fix: GPR curation for fatty_acid_oxidation and Glycerolipid_metabolism
JHL-452b Dec 4, 2024
498495a
chore: add macaw test result
JHL-452b Dec 4, 2024
98b3400
Merge remote-tracking branch 'origin/develop' into Fix-Fatty_acid_oxi…
edkerk Dec 17, 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 #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.
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24 changes: 12 additions & 12 deletions model/Human-GEM.yml
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Expand Up @@ -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"
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- 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"
Expand Down Expand Up @@ -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"
Expand All @@ -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"
Expand Down Expand Up @@ -223519,7 +223519,7 @@
- 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"
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- 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"
Expand Down Expand Up @@ -232327,7 +232327,7 @@
- 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"
Expand Down Expand Up @@ -237386,7 +237386,7 @@
- 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: ""
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- 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: ""
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- 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: ""
Expand Down Expand Up @@ -241211,7 +241211,7 @@
- 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: ""
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- 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"
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