Fix: GPR curation for transport reactions (3)

[JHL-452b]

Main improvements in this PR:

As proposed in #916 #917 #919 #922 #925 #920 :

• Remove ENSG00000170522, ENSG00000026652, ENSG00000125505, ENSG00000197977, ENSG00000123684, ENSG00000186792, ENSG00000100344, ENSG00000143797, ENSG00000176454, ENSG00000146648, ENSG00000141446, ENSG00000160216, ENSG00000012660, ENSG00000111684, ENSG00000102125 from MAR00158;
• Remove ENSG00000135917 from MAR00095;
• Remove ENSG00000113396 from MAR00164;
• Remove ENSG00000165029 from MAR00198;
• Remove ENSG00000103569 from MAR01485;
• Remove ENSG00000130821, ENSG00000130822 from MAR03011;
• Remove ENSG00000130821 from MAR03013;
• Remove ENSG00000108932 from MAR04930;
• Remove ENSG00000123643 from MAR05048;
• Remove ENSG00000123643 from MAR05051;
• Remove ENSG00000123643 from MAR05062;
• Remove ENSG00000107819 from MAR07759;
• Remove ENSG00000125454 from MAR07835;
• Remove ENSG00000125454 from MAR07837;
• Remove ENSG00000125454 from MAR07838;
• Remove ENSG00000125454 from MAR07839;
• Remove ENSG00000125454 from MAR07840;
• Remove ENSG00000125454 from MAR07841;
• Remove ENSG00000125454 from MAR07842;
• Remove ENSG00000125454 from MAR07843;
• Remove ENSG00000125454 from MAR07845;
• Remove ENSG00000125454 from MAR07846;
• Remove ENSG00000125454 from MAR07847;
• Remove ENSG00000125454 from MAR07849;
• Remove ENSG00000125454 from MAR07850;
• Remove ENSG00000125454 from MAR07851;
• Remove ENSG00000125454 from MAR07852;
• Remove ENSG00000125454 from MAR07853;
• Remove ENSG00000125454 from MAR07854;
• Remove ENSG00000152779, ENSG00000165449 from MAR08496;
• Remove ENSG00000115902 from MAR08972;
• Remove ENSG00000149150, ENSG00000167703 from MAR09274;
• Remove ENSG00000005471, ENSG00000121270 from MAR09882;
• Remove ENSG00000085563 from MAR11768;
• Remove ENSG00000015520 from MAR11815;
• Remove ENSG00000073734 from MAR12184;
• Remove ENSG00000184343, ENSG00000130821 from MAR03014;
• Remove ENSG00000117620, ENSG00000205060 from MAR08857;
• Remove ENSG00000174669, ENSG00000112759 from MAR11801;
• Remove ENSG00000130821, ENSG00000184343, ENSG00000130822 from MAR03008;
• Remove ENSG00000130821, ENSG00000184343 from MAR03017;
• Remove ENSG00000186198, ENSG00000163959 from MAR12185;
• Remove ENSG00000130958, ENSG00000117620 from MAR00918;
• Remove ENSG00000102125 and ENSG00000117620 from the model as they are not connected to any reactions after this curation.

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]

Remove ENSG00000170522, ENSG00000026652, ENSG00000125505, ENSG00000197977, ENSG00000123684, ENSG00000186792, ENSG00000100344, ENSG00000143797, ENSG00000176454, ENSG00000146648, ENSG00000141446, ENSG00000160216, ENSG00000012660, ENSG00000111684, ENSG00000102125 from MAR00158;

ENSG00000146648 has already been removed in the develop branch.

[JHL-452b]

Reaction ID	issues
MAR00158	916, 919, 922, 925
MAR00095, MAR00164, MAR00198, MAR01485, MAR03011, MAR03013, MAR04930, MAR05048, MAR05051, MAR05062, MAR07759, MAR07835, MAR07837, MAR07838, MAR07839, MAR07840, MAR07841, MAR07842, MAR07843, MAR07845, MAR07846, MAR07847, MAR07849, MAR07850, MAR07851, MAR07852, MAR07853, MAR07854, MAR08496, MAR08972, MAR09274, MAR09882, MAR11768, MAR11815, MAR12184	917
MAR03014, MAR08857, MAR11801	917, 920
MAR03008	917, 920, 922
MAR03017, MAR12185	917, 922
MAR00918	917, 925

In this PR, the main focus is on the reactions related to 917. Among these reactions, some have also been mentioned in other issues. To avoid conflicts, duplicate reactions mentioned in other issues are also being addressed and curated here together. For specific details, refer to the content in the table above.

[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    2145     84    271    0.86078       0.15576        0.96231       0.21978     0.17554
    {'GBM'   }    57    2135     77    280    0.85995       0.16914        0.96519       0.24204     0.20388
    {'HCT116'}    71    2177     69    288    0.86296       0.19777        0.96928       0.28457     0.25534
    {'HELA'  }    35    2217    105    250    0.86383       0.12281        0.95478       0.16471      0.1074
    {'RPE1'  }    21    2160    113    255    0.85563      0.076087        0.95029       0.10244     0.03672
    {'all'   }     8    2354    132    113    0.90602      0.066116         0.9469      0.061303    0.012149

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