Remove peroxisomal genes from mitochondrial ACAD reactions

[Devlin-Moyer]

Main improvements in this PR:

As proposed in #634:

• Sets the GPRs of MAR01253 and MAR01270 to ENSG00000072778 or ENSG00000115361 or ENSG00000177646
• Sets the GPR of MAR03997 to ENSG00000072778 or ENSG00000115361
• Sets the GPR of MAR03291 to ENSG00000115361
• Sets the GPRs of MAR03163 and MAR03212 to ENSG00000122971 or ENSG00000151498 or ENSG00000196177

Since the above changes would leave ENSG00000240303 associated with no reactions, also

• adds ENSG00000240303 to the GPRs of MAR03107 and MAR03111
• adds PMID:21237683 to the references for MAR03107 and MAR03111

Since this already edits the GPRs for MAR03107 and MAR03111, also removes ENSG00000117054 from those GPRs, as suggested in #980, and adds it to the GPRs of MAR03752 and MAR03784 to ensure that it is still associated with at least one reaction

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

[github-actions]

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.

[Devlin-Moyer]

looks like MAR01253 and MAR01270 were the only two reactions that ENSG00000240303 (ACAD11) was associated with; according to this paper, it is capable of dehydrogenating acyl-CoAs with 20-26 carbons in their primary chains, so I'll put together a list of other reactions it could be associated with

[Devlin-Moyer]

MAR03111 represents the dehydrogenation of eicosanoyl-CoA (20 carbons in primary chain), and MAR03107 represents the dehydrogenation of docosanoyl-CoA (22 carbons), so I'm adding ENSG00000240303 to both GPRs and PMID:21237683 to both reactions' lists of references. I am intentionally skipping MAR00869 because I proposed to remove it in #798

[github-actions]

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.

[JHL-452b]

It looks good to me! 😄

[Devlin-Moyer]

the YAML validation is failing because MAR03107 and MAR03111 were apparently the only two reactions that ACAD8 (ENSG00000117054) was associated with. I made that change because of #980, which also mentions that ACAD8 is capable of acting on isobutyryl-CoA and 2-methylbutyryl-CoA, which are represented by MAR03752 and MAR03784, respectively, so I'll also add ACAD8 to the GPRs of those reactions