fix: GPR curation for Transport reactions (2)

[JHL-452b]

Main improvements in this PR:

As proposed in #916

• Remove ENSG00000165449 from MAR05292;
• Remove ENSG00000100075 from MAR06289;
• Remove ENSG00000100075 from MAR06296;
• Remove ENSG00000125454 from MAR06332;
• Remove ENSG00000125454 from MAR06333;
• Remove ENSG00000125454 from MAR06334;
• Remove ENSG00000125454 from MAR06336;
• Remove ENSG00000125454 from MAR06337;
• Remove ENSG00000125454 from MAR06339;
• Remove ENSG00000125454 from MAR06340;
• Remove ENSG00000125454 from MAR06341;
• Remove ENSG00000125454 from MAR06342;
• Remove ENSG00000125454 from MAR06343;
• Remove ENSG00000125454 from MAR07804;
• Remove ENSG00000125454 from MAR07810;
• Remove ENSG00000125454 from MAR07812;
• Remove ENSG00000125454 from MAR07814;
• Remove ENSG00000125454 from MAR07818;
• Remove ENSG00000125454 from MAR07822;
• Remove ENSG00000125454 from MAR07824;
• Remove ENSG00000125454 from MAR07826;
• Remove ENSG00000125454 from MAR07828;
• Remove ENSG00000125454 from MAR07829;
• Remove ENSG00000125454 from MAR07830;
• Remove ENSG00000125454 from MAR07832;
• Remove ENSG00000125454 from MAR07833;
• Remove ENSG00000125454 from MAR07834;
• Remove ENSG00000059804 from MAR08586;
• Remove ENSG00000117834 from MAR08876;
• Remove ENSG00000066230, ENSG00000115616, ENSG00000090020 from MAR08925;
• Remove ENSG00000113396 from MAR08941;
• Remove ENSG00000196517 from MAR09591;
• Remove ENSG00000196517 from MAR09592;
• Remove ENSG00000196517 from MAR09593;
• Remove ENSG00000196517 from MAR09594;
• Remove ENSG00000196517 from MAR09595;
• Remove ENSG00000196517 from MAR09598;
• Remove ENSG00000196517 from MAR09599;
• Remove ENSG00000196517 from MAR09600;
• Remove ENSG00000196517 from MAR09601;

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.

[hhl-24]

LGTM!

[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    2144     84    271    0.86073       0.15576         0.9623       0.21978     0.17551
    {'GBM'   }    57    2134     77    280    0.85989       0.16914        0.96517       0.24204     0.20385
    {'HCT116'}    71    2176     69    288     0.8629       0.19777        0.96927       0.28457     0.25532
    {'HELA'  }    35    2216    105    250    0.86378       0.12281        0.95476       0.16471     0.10737
    {'RPE1'  }    21    2159    113    255    0.85557      0.076087        0.95026       0.10244    0.036689
    {'all'   }     8    2353    132    113    0.90599      0.066116        0.94688      0.061303    0.012129

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