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Fix: GPR curation for Sphingolipid metabolism #946

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merged 2 commits into from
Jan 8, 2025

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JHL-452b
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Main improvements in this PR:

As proposed in #860

  • Remove ENSG00000101577, ENSG00000132793, ENSG00000134324 from MAR00746;
  • Remove ENSG00000102595, ENSG00000175711, ENSG00000147162, ENSG00000180549, ENSG00000069943, ENSG00000172461, ENSG00000198488, ENSG00000170340, ENSG00000196371, ENSG00000136731, ENSG00000172728, ENSG00000085998, ENSG00000167889 from MAR00765;
  • Remove ENSG00000101577 from MAR00767;
  • Remove ENSG00000134324 from MAR00775;
  • Remove ENSG00000179913 from MAR08152;
  • Remove ENSG00000179913 from MAR08173;
  • Remove ENSG00000179913 from MAR08249.

I hereby confirm that I have:

  • Tested my code on my own computer for running the model
  • Selected develop as a target branch
  • Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

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This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
- Found 1523 dead-end metabolites.
- Found 1328 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 1975 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
- Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
- Found 447 reactions that were some type of duplicate:
- 0 were completely identical to at least one other reaction.
- 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
- 447 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/macawResults/.

Note: In the case of multiple test runs, this post will be edited.

@feiranl feiranl requested a review from hhl-24 December 25, 2024 01:22
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I have tested it using MATLAB, but I have encounted some inconsistencies.

@feiranl feiranl merged commit 5ee3092 into develop Jan 8, 2025
@feiranl feiranl deleted the Fix-Sphingolipid_metabolism branch January 8, 2025 14:13
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3 participants