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fix: remove duplicate krebs cycle rxns of PDH and OGDH #541

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merged 7 commits into from
Apr 28, 2023

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@haowang-bioinfo haowang-bioinfo commented Apr 24, 2023

Main improvements in this PR:

This PR resolves duplicate reactions of PDH and OGDH by only keeping the highest resolution versions, as discussed in #524

  • remove lumped PDH and OGDH reactions MAR04137 and MAR05297
  • remove medium resolution version decarboxylation reactions of PDH and OGDH
  • convert MAR08746, as well as MAM00561 from cytosol to mitochondrion
  • add new reaction MAR20069 that converts mitochondrial 2-(alpha-hydroxyethyl)thiamine-diphosphate and lipoamide into S-acetyldihydrolipoamide and thiamin-PP
  • modify GPRs for PDH reactions:
    • MAR20069: (ENSG00000131828 and ENSG00000168291) or (ENSG00000163114 and ENSG00000168291) (ENSG00000131828 and ENSG00000168291 and ENSG00000150768) or (ENSG00000163114 and ENSG00000168291 and ENSG00000150768)
    • MAR06412: ENSG00000110435 (PDHX) and ENSG00000150768 (DLAT)

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

- remove reactions MAR06410 and MAR06411, and retain the high-resolution version
- this new reaction converts mitochondrial 2-(alpha-hydroxyethyl)thiamine-diphosphate and lipoamide into S-acetyldihydrolipoamide and thiamin-PP
@haowang-bioinfo haowang-bioinfo marked this pull request as ready for review April 25, 2023 06:29
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@all-contributors please add @Devlin-Moyer and @juliette-cooke for the bug report.

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@haowang-bioinfo

I've put up a pull request to add @Devlin-Moyer! 🎉

MAR20069: (ENSG00000131828 and ENSG00000168291) or (ENSG00000163114 and ENSG00000168291)
MAR06412: ENSG00000110435 and ENSG00000150768
model/Human-GEM.yml Show resolved Hide resolved
@haowang-bioinfo haowang-bioinfo merged commit 3fd17f4 into develop Apr 28, 2023
@haowang-bioinfo haowang-bioinfo deleted the fix/removeDuplicateKrebsCycleRxns branch April 28, 2023 08:46
@haowang-bioinfo haowang-bioinfo mentioned this pull request May 7, 2023
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2 participants