fix: GPR curation for transport reactions (10)

[JHL-452b]

Main improvements in this PR:

As proposed in #910 #911 #912 #919 #921 #922 #925

• Remove ENSG00000100156, ENSG00000108932 from MAR06000;
• Remove ENSG00000100156, ENSG00000141526 from MAR06001;
• Remove ENSG00000155380, ENSG00000100156, ENSG00000108932, ENSG00000141526, ENSG00000118596 from MAR06002;
• Remove ENSG00000108932, ENSG00000141526, ENSG00000118596, ENSG00000100156, ENSG00000155380 from MAR06005;
• Remove ENSG00000100156, ENSG00000141526, ENSG00000108932 from MAR06010;
• Remove ENSG00000108932, ENSG00000141526 from MAR06003;
• Remove ENSG00000108932, ENSG00000100156, ENSG00000141526 from MAR06006;
• Remove ENSG00000108932, ENSG00000141526, ENSG00000100156 from MAR06009;
• Remove ENSG00000155380, ENSG00000108932, ENSG00000141526 from MAR06012;
• Remove ENSG00000100156, ENSG00000141526, ENSG00000108932 from MAR06008;
• Remove ENSG00000108932 from MAR06014;
• Remove ENSG00000108932 from MAR06017;
• Remove ENSG00000108932 from MAR06018;
• Remove ENSG00000108932 from MAR06019;
• Remove ENSG00000108932 from MAR06021;
• Remove ENSG00000108932 from MAR06026;
• Remove ENSG00000100156, ENSG00000108932 from MAR06030;
• Remove ENSG00000100156, ENSG00000108932, ENSG00000141526, ENSG00000118596 from MAR06031;
• Remove ENSG00000100156, ENSG00000108932, ENSG00000141526 from MAR06032;
• Remove ENSG00000108932 from MAR06033;
• Remove ENSG00000100156, ENSG00000108932, ENSG00000141526 from MAR06034;
• Remove ENSG00000155380, ENSG00000100156, ENSG00000108932, ENSG00000141526 from MAR06035;
• Remove ENSG00000100156, ENSG00000108932, ENSG00000141526 from MAR06036;
• Remove ENSG00000100156, ENSG00000108932, ENSG00000141526, ENSG00000118596 from MAR06037;
• Remove ENSG00000108932, ENSG00000141526 from MAR06016;
• Remove ENSG00000100156, ENSG00000141526, ENSG00000108932 from MAR06022;
• Remove ENSG00000141526, ENSG00000100156 from MAR06029;
• Remove ENSG00000100156, ENSG00000118596, ENSG00000141526, ENSG00000108932 from MAR06027;
• Remove ENSG00000108932, ENSG00000141526, ENSG00000118596 from MAR06013;
• Remove ENSG00000108932, ENSG00000100156 from MAR06015;
• Remove ENSG00000141526, ENSG00000108932 from MAR06023;
• Remove ENSG00000155380, ENSG00000108932, ENSG00000141526, ENSG00000118596, ENSG00000100156 from MAR06028;
• Remove ENSG00000100156, ENSG00000108932, ENSG00000141526 from MAR06024;
• Remove ENSG00000141526, ENSG00000108932 from MAR06025.

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

[JHL-452b]

Reaction ID	issues
MAR06000, MAR06001, MAR06002	910
MAR06005, MAR06010	910, 919, 922
MAR06003	910, 921
MAR06006, MAR06009, MAR06012	910, 922
MAR06008	910, 925
MAR06014, MAR06017, MAR06018, MAR06019, MAR06021, MAR06026, MAR06030, MAR06031, MAR06032, MAR06033, MAR06034, MAR06035, MAR06036	911
MAR06037	911, 912, 922
MAR06016, MAR06022, MAR06029	911, 919
MAR06027	911, 919, 922
MAR06013, MAR06015, MAR06023, MAR06028	911, 922
MAR06024, MAR06025	911, 925

In this PR, the main focus is on the reactions related to 910 and 911. 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    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.