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fix: GPR curation for Arachidonic acid metabolism #962

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merged 5 commits into from
Jan 9, 2025

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JHL-452b
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@JHL-452b JHL-452b commented Jan 8, 2025

Main improvements in this PR:

As proposed in #853 #854 :

  • Remove ENSG00000186377 from MAR02043, MAR01195, MAR02457, MAR02456, MAR00951, MAR07940, MAR02033, MAR00946, MAR00950, MAR00992, MAR03788, MAR00947, MAR01151, MAR01152, MAR00994, MAR01155, MAR02031, MAR01154, MAR02029, MAR00933, MAR00937, MAR02458, MAR01149, MAR01193, MAR00993, MAR02034, MAR00948, MAR02053, MAR02455, MAR07957, MAR00934, MAR00938, MAR00939, MAR00942, MAR01153, MAR00931, MAR00932, MAR07941, MAR02032, MAR01150, MAR02030, MAR06657, MAR00940, MAR00936, MAR00943, MAR00991, MAR04051, MAR00935, MAR01156, MAR04055, MAR04090, MAR01196, MAR02042, MAR02054, MAR00944, MAR01194;
  • Remove ENSG00000242110 from MAR01067;
  • Remove ENSG00000197408 from MAR00932.

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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github-actions bot commented Jan 8, 2025

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.

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@feiranl feiranl left a comment

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LGTM! Except ”Remove ENSG00000162365 from MAR00934“ mentioned in #853 is missing.

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github-actions bot commented Jan 8, 2025

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

     cellLine     TP     TN     FP     FN     accuracy    sensitivity    specificity       F1         MCC   
__________ __ ____ ___ ___ ________ ___________ ___________ ________ ________

{'DLD1' } 50 2147 85 272 0.86022 0.15528 0.96192 0.21882 0.17386
{'GBM' } 57 2138 78 280 0.85977 0.16914 0.9648 0.24153 0.20259
{'HCT116'} 71 2179 70 289 0.8624 0.19722 0.96888 0.28343 0.25335
{'HELA' } 35 2219 106 251 0.86327 0.12238 0.95441 0.16393 0.1061
{'RPE1' } 21 2163 114 255 0.85546 0.076087 0.94993 0.10219 0.036105
{'all' } 8 2357 133 113 0.90578 0.066116 0.94659 0.061069 0.011814

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

@feiranl feiranl merged commit c0ba199 into develop Jan 9, 2025
5 of 6 checks passed
@feiranl feiranl deleted the Fix-Arachidonic_acid_metabolism branch January 9, 2025 14:28
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2 participants