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add Alpha subunits of sodium channel genes to MAR01527 #664

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merged 12 commits into from
Aug 3, 2023

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Devlin-Moyer
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@Devlin-Moyer Devlin-Moyer commented Jun 21, 2023

Main improvements in this PR:

As proposed in #583, replaces the existing GPR of MAR01527 with ENSG00000144285 or ENSG00000136531 or ENSG00000153253 or ENSG00000007314 or ENSG00000183873 or ENSG00000136546 or ENSG00000196876 or ENSG00000169432 or ENSG00000185313 or ENSG00000168356 or ENSG00000164588 or ENSG00000138622 or ENSG00000186815 or ENSG00000162341 or ENSG00000102452 or (ENSG00000111319 and ENSG00000168447 and ENSG00000166828) or ENSG00000162572 (see these papers re: the ANDed genes near the end; these have been added to the list of references for MAR01527)
Also adds new gene entries for all of those genes, since none were already in Human-GEM

Sodium channels consist of large alpha subunits that associate with accessory proteins, such as beta subunits. An alpha subunit forms the core of the channel and is functional on its own. When the alpha subunit protein is expressed by a cell, it is able to form a pore in the cell membrane that conducts Na+ in a voltage-dependent way, even if beta subunits or other known modulating proteins are not expressed. When accessory proteins assemble with α subunits, the resulting complex can display altered voltage dependence and cellular localization. Note that all these added genes encode alpha subunits of sodium channel, except SCNN1A, B, D, G that encode subunits alpha, beta, delta, and gamma of sodium channel epithelial 1, respectively none of them encode beta subunit.

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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I can't tell why the YAML validation is failing; in the past, that error message has indicated that there's a gene in Human-GEM.yml that isn't in genes.tsv or visa versa, but as far as I can tell, all genes in genes.tsv are in Human-GEM.yml and visa versa. I'm just gonna wait until this PR is merged and see if those changes to the automated tests make the situation any clearer

@mihai-sysbio mihai-sysbio force-pushed the fix/sodium_channel_genes branch 2 times, most recently from 45617e1 to 87fdb2b Compare July 10, 2023 17:42
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Through commit 8cb8f78 the output of the errors was more detailed, but the side-effect of that is that the reported error is now gone, as expected.

@haowang-bioinfo haowang-bioinfo mentioned this pull request Aug 1, 2023
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@haowang-bioinfo haowang-bioinfo changed the title Add Sodium Channel Genes to MAR01527 add Alpha subunits of sodium channel genes to MAR01527 Aug 1, 2023
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PR message is updated and specified that only alpha subunits are added

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haowang-bioinfo commented Aug 2, 2023

5 new genes were added , what are they? and why? - this info is missing, should be explicitly documented in #583 or #664 and they were mentioned in #583, where I gave some comments

@haowang-bioinfo haowang-bioinfo merged commit 0745ddf into develop Aug 3, 2023
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@haowang-bioinfo haowang-bioinfo deleted the fix/sodium_channel_genes branch August 3, 2023 21:06
@haowang-bioinfo haowang-bioinfo mentioned this pull request Sep 25, 2023
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3 participants