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fix: GPRs for mitochondrial 2-enoyl-CoA hydratase reactions #808

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merged 4 commits into from
Apr 24, 2024

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Devlin-Moyer
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Main improvements in this PR:

As proposed in #757:

  • Changes GPRs of MAR01163, MAR01177, MAR01182, MAR01206, MAR01219, MAR01224, MAR01255, MAR01272, MAR03108, MAR03112, MAR03116, MAR03122, MAR03129, MAR03171, MAR03175, MAR03179, MAR03183, MAR03187, MAR03219, MAR03223, MAR03227, MAR03231, MAR03235, MAR03241, MAR03245, MAR03252, MAR03260, MAR03277, MAR03281, MAR03285, MAR03449, and MAR03453 to ENSG00000084754 (HADHA)
  • Changes GPRs of MAR03136, MAR03143, MAR03150, MAR03157, MAR03191, MAR03195, MAR03199, MAR03290, MAR03523, and MAR03528 to ENSG00000084754 or ENSG00000127884 (HADHA or ECHS1)
  • Changes GPRs of MAR03164, MAR03203, MAR03532, MAR03753, MAR03785, and MAR04735 to ENSG00000127884 (ECHS1)

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

@Devlin-Moyer Devlin-Moyer linked an issue Feb 23, 2024 that may be closed by this pull request
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@feiranl feiranl self-requested a review March 19, 2024 02:43
model/Human-GEM.yml Outdated Show resolved Hide resolved
@JHL-452b
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JHL-452b commented Apr 7, 2024

LGTM!

@feiranl
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feiranl commented Apr 23, 2024

According to the model yaml file, it seems that grRules for rxn MAR03281 hasn't been changed as said. It is still 'ENSG00000084754 and ENSG00000113790 and ENSG00000127884'. Please double check this @Devlin-Moyer
Thanks! If you double checked it is correct, I can commit to fix the issue, since right now this PR has some conflict in yml file.

@Devlin-Moyer
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yep it looks like I missed MAR03281; I've corrected that and also taken care of the merge conflict with the develop branch that showed up

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LGTM!

@feiranl feiranl merged commit 56279d7 into develop Apr 24, 2024
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@feiranl feiranl deleted the fix/remove_EHHADH_from_mito_gprs branch April 24, 2024 01:21
@JHL-452b JHL-452b mentioned this pull request May 30, 2024
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GPRs for Mitochondrial 2-enoyl-CoA Hydration Reactions
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