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Remove lipid droplet breakdown reaction MAR00032 #658

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merged 3 commits into from
Jul 2, 2023

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Devlin-Moyer
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@Devlin-Moyer Devlin-Moyer commented Jun 20, 2023

Main improvements in this PR:

Removes MAR00032 and associated non-metabolic genes ENSG00000072062, ENSG00000142875, ENSG00000165059, ENSG00000172531, ENSG00000186298, and ENSG00000213639, as proposed in #631

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
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Apparently MAR00032 was the only reaction that ENSG00000072062, ENSG00000142875, ENSG00000165059, ENSG00000172531, ENSG00000186298, and ENSG00000213639 were associated with (that's why the YAML validation failed); @JonathanRob, since you mentioned that some of the gene associations with MAR00030 were questionable, have you maybe already determined that any/all of these genes should be removed from Human-GEM entirely?

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Yes, it's fine to remove these genes from the model altogether.

@haowang-bioinfo
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haowang-bioinfo commented Jul 2, 2023

Yes, it's fine to remove these genes from the model altogether.

these 6 genes encode either kinases or phosphatases that undertake regulatory activities, instead of lipid droplet formation.

@haowang-bioinfo haowang-bioinfo changed the title Remove MAR00032 Remove lipid droplet breakdown reaction MAR00032 Jul 2, 2023
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the questionable GPR of MAR00032 supports its removal

@haowang-bioinfo haowang-bioinfo merged commit ca1d328 into develop Jul 2, 2023
@haowang-bioinfo haowang-bioinfo deleted the fix/remove_lipid_droplet_loop branch July 2, 2023 17:57
@haowang-bioinfo haowang-bioinfo mentioned this pull request Sep 25, 2023
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3 participants