fix: GPR curation for Transport reactions (1)

[JHL-452b]

Main improvements in this PR:

As proposed in #900 , #912 , #917 , #920 , #925 , #924 , #919

• Remove ENSG00000143554 from MAR00155;
• Remove ENSG00000113396 from MAR00191;
• Remove ENSG00000165029 from MAR00295;
• Remove ENSG00000165029 from MAR00311;
• Remove ENSG00000165029 from MAR00317;
• Remove ENSG00000165029 from MAR00335;
• Remove ENSG00000165029 from MAR00355;
• Remove ENSG00000165029 from MAR00375;
• Remove ENSG00000165029 from MAR00391;
• Remove ENSG00000165029 from MAR00415;
• Remove ENSG00000140284 from MAR01665;
• Remove ENSG00000021488 from MAR01901;
• Remove ENSG00000021488 from MAR01903;
• Remove ENSG00000021488 from MAR01906;
• Remove ENSG00000021488 from MAR01907;
• Remove ENSG00000021488 from MAR01908;
• Remove ENSG00000147606, ENSG00000091138 from MAR01914;
• Remove ENSG00000136856 from MAR04858;
• Remove ENSG00000125454 from MAR04933;
• Remove ENSG00000141526 from MAR04976;
• Remove ENSG00000165349, ENSG00000155465, ENSG00000139514, ENSG00000003989 from MAR05073;
• Remove ENSG00000107159, ENSG00000164879, ENSG00000074410, ENSG00000133742, ENSG00000168748, ENSG00000185015, ENSG00000104267, ENSG00000118298, ENSG00000131686, ENSG00000167434, ENSG00000165029, ENSG00000169239 from MAR00190;
• Remove ENSG00000021488, ENSG00000084453 from MAR01905;
• Remove ENSG00000003989, ENSG00000167703, ENSG00000165349, ENSG00000139514 from MAR05074;
• Remove ENSG00000108932, ENSG00000100156 from MAR05018;
• Remove ENSG00000149150, ENSG00000167703, ENSG00000139514 from MAR05070;
• Remove ENSG00000108932 from MAR06038;
• Remove ENSG00000108932 from MAR06042;
• Remove ENSG00000108932, ENSG00000141526 from MAR06047;
• Remove ENSG00000108932 from MAR06049;
• Remove ENSG00000108932, ENSG00000141526 from MAR06050;
• Remove ENSG00000174640 from MAR06218;
• Remove ENSG00000174640 from MAR06223;
• Remove ENSG00000146477 from MAR06247;
• Remove ENSG00000146477 from MAR06247;
• Remove ENSG00000180773 from MAR06371;
• Remove ENSG00000180773 from MAR06374;
• Remove ENSG00000165349, ENSG00000139514, ENSG00000003989 from MAR06379;
• Remove ENSG00000165349, ENSG00000139514, ENSG00000003989 from MAR06383;
• Remove ENSG00000108932, ENSG00000141526, ENSG00000100156 from MAR06043;
• Remove ENSG00000118596, ENSG00000108932, ENSG00000141526 from MAR06053;
• Remove ENSG00000108932, ENSG00000141526, ENSG00000118596, ENSG00000155380, ENSG00000100156 from MAR06039;
• Remove ENSG00000108932, ENSG00000141526, ENSG00000118596, ENSG00000155380, ENSG00000100156 from MAR06040;
• Remove ENSG00000067113, ENSG00000072756, ENSG00000139505, ENSG00000141934, ENSG00000163082, ENSG00000063601, ENSG00000126821 from MAR06512;
• Remove ENSG00000155380, ENSG00000100156, ENSG00000108932, ENSG00000118596, ENSG00000141526 from MAR06051;
• Remove ENSG00000155380, ENSG00000108932, ENSG00000141526, ENSG00000118596 from MAR06044;
• Remove ENSG00000108932, ENSG00000141526, ENSG00000100156 from MAR06045;
• Remove ENSG00000141526, ENSG00000108932 from MAR06046;
• Remove ENSG00000100156, ENSG00000108932, ENSG00000155380 from MAR06052;
• Remove ENSG00000100156, ENSG00000108932, ENSG00000141526 from MAR06041;
• Remove ENSG00000118596, ENSG00000141526, ENSG00000155380 from MAR08364;
• Remove ENSG00000072756 and ENSG00000163082 from 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.

[JHL-452b]

Remove ENSG00000072756 and ENSG00000163082 from model as they are not connected to any reactions after this curation.

Of the two genes planned to be removed, the main function of ENSG00000072756 (TRNT1) is to synthesize tRNA and thus participate in the translation process, while the main function of ENSG00000163082 (SGPP2) is to encode the phosphatase of Sphingosine-1-phosphate. Therefore, I think it is reasonable to remove ENSG00000072756 from the model, while the function of ENSG00000163082 is consistent with the reaction MAR00775, and it is recommended to be retained in the model as part of the GPR of MAR00775.

[hhl-24]

Remove ENSG00000113396 from MAR00191;

As proposed in 900, keep ENSG00000113396 for MAR00191.

As proposed in #900 , #912 , #917 , #920 , #925 , #924 , #919

I found some are proposed in 918 and 922. For example, Remove ENSG00000155380 from MAR06052(in 922), Remove ENSG00000167703 from MAR05074(in 918).

Others look good to me.

[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     85    272    0.86011       0.15528        0.96188       0.21882     0.17381
    {'GBM'   }    57    2136     78    280    0.85966       0.16914        0.96477       0.24153     0.20253
    {'HCT116'}    71    2178     70    288    0.86268       0.19777        0.96886         0.284     0.25386
    {'HELA'  }    35    2218    106    250    0.86355       0.12281        0.95439       0.16432      0.1065
    {'RPE1'  }    21    2161    114    255    0.85535      0.076087        0.94989       0.10219    0.036043
    {'all'   }     8    2355    133    113    0.90571      0.066116        0.94654      0.061069    0.011774

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

[hhl-24]

LGTM!