Fix-GPR curation for fatty_acid_oxidation and Glycerolipid_metabolism

[JHL-452b]

Main improvements in this PR:

As proposed in #848

• Remove ENSG00000196344 from MAR00453;
• Remove ENSG00000196616, ENSG00000196344 from MAR00458;
• Remove ENSG00000169169 from MAR01488;
• Remove ENSG00000161533 from MAR03291;
• Remove ENSG00000068366, ENSG00000103740, ENSG00000119673, ENSG00000123983, ENSG00000130377, ENSG00000151726, ENSG00000164398, ENSG00000177465, ENSG00000197142 from MAR03387, and only keep ENSG00000140284;
• Remove ENSG00000169169 from MAR04457;
• Remove ENSG00000169169 from MAR04711;
• Remove ENSG00000135929 from MAR04838;
• Remove ENSG00000135929 from MAR04839;
• Remove ENSG00000169169 from MAR06278;
• Change the GPR of MAR06285 into (ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835) and (ENSG00000060971 or ENSG00000116171);
• Change the GPR of MAR11539 into (ENSG00000161533 or ENSG00000087008) and (ENSG00000113790 or ENSG00000133835)

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 1514 dead-end metabolites.
 - Found 1319 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1977 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.

[feiranl]

LGTM except the GPR for MAR06285 and MAR11539. Those two seems strange to me, please double check.

[hhl-24]

The substrates for peroxisomal β-oxidation primarily include very long-chain fatty acids (VLCFA) (≥C22), long-chain fatty acids, and branched-chain fatty acids (BCFA) . However, the fatty acids involved in MAR06285 and MAR11539 are medium- and short-chain fatty acids, so these reactions should occur in the mitochondria rather than in the peroxisomes.

[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'  }    36    2181    61    279    0.86703       0.11429        0.97279       0.17476     0.14981
    {'GBM'   }    34    2161    63    298    0.85876       0.10241        0.97167       0.15851     0.13034
    {'HCT116'}    45    2202    56    310    0.85993       0.12676         0.9752       0.19737     0.18123
    {'HELA'  }    30    2260    71    253    0.87605       0.10601        0.96954       0.15625      0.1218
    {'RPE1'  }    15    2201    82    258    0.86698      0.054945        0.96408      0.081081    0.030757
    {'all'   }     7    2404    94    109    0.92234      0.060345        0.96237      0.064516     0.02427

Note: In the case of multiple test runs, this post will be edited.