Fix: GPR curation for transport reactions (5)

[JHL-452b]

Main improvements in this PR:

As proposed in #920 and #921 :

• Remove ENSG00000165029 from MAR00215;
• Remove ENSG00000165029 from MAR00231;
• Remove ENSG00000165029 from MAR00239;
• Remove ENSG00000165029 from MAR00269;
• Remove ENSG00000165029 from MAR00277;
• Remove ENSG00000165029 from MAR00287;
• Remove ENSG00000165029 from MAR00351;
• Remove ENSG00000021488 from MAR01902;
• Remove ENSG00000021488 from MAR01904;
• Remove ENSG00000205060 from MAR04125;
• Remove ENSG00000108932 from MAR04935;
• Remove ENSG00000103257 from MAR05467;
• Remove ENSG00000165029 from MAR05540;
• Remove ENSG00000103257 from MAR05575;
• Remove ENSG00000103257 from MAR05588;
• Remove ENSG00000103064 from MAR05606;
• Remove ENSG00000102743 from MAR06314;
• Remove ENSG00000125454 from MAR07827;
• Remove ENSG00000125454 from MAR07836;
• Remove ENSG00000125454 from MAR07844;
• Remove ENSG00000100170 from MAR11410;
• Remove ENSG00000165970 from MAR11456;
• Remove ENSG00000173638 from MAR11647;
• Remove ENSG00000142583 from MAR11779;
• Remove ENSG00000103064 from MAR05608;
• Remove ENSG00000103064 from MAR05615;
• Remove ENSG00000103064 from MAR05627;
• Remove ENSG00000103064 from MAR05640;
• Remove ENSG00000103064 from MAR05653;
• Remove ENSG00000103064 from MAR05659;
• Remove ENSG00000103064 from MAR05675;
• Remove ENSG00000103064 from MAR05686;
• Remove ENSG00000103064 from MAR05690;
• Remove ENSG00000103064 from MAR05696;
• Remove ENSG00000103064 from MAR05717;
• Remove ENSG00000103064 from MAR05720;
• Remove ENSG00000103064 from MAR05734;
• Remove ENSG00000103064 from MAR05741;
• Remove ENSG00000103064 from MAR05742;
• Remove ENSG00000103064 from MAR05744;
• Remove ENSG00000103064 from MAR05749;
• Remove ENSG00000103064 from MAR05766;
• Remove ENSG00000103064 from MAR05787;
• Remove ENSG00000103064 from MAR05799;
• Remove ENSG00000103064 from MAR05801;
• Remove ENSG00000103064 from MAR05810;
• Remove ENSG00000103064 from MAR05811;
• Remove ENSG00000103064 from MAR05815;
• Remove ENSG00000103064 from MAR05825;
• Remove ENSG00000103064 from MAR05831;
• Remove ENSG00000103064 from MAR05856;
• Remove ENSG00000103064 ENSG00000108932 from MAR05998;

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 ENSG00000103064 from MAR05998

The gene ENSG00000103064 is not present in the GPR of MAR05998. Others look good to me.

[JHL-452b]

This is an editing error; I actually removed ENSG00000108932 from MAR05998.

[hhl-24]

Remove ENSG00000103064 from MAR05606

In fact, I found that the gene that was removed was not ENSG00000103064, but ENSG00000103257.

[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.

[hhl-24]

LGTM!

[JHL-452b]

Reaction ID	issues
MAR00215, MAR00231, MAR00239, MAR00269, MAR00277, MAR00287, MAR00351, MAR01902, MAR01904, MAR04125, MAR04935, MAR05467, MAR05540, MAR05575, MAR05588, MAR05606, MAR06314, MAR07827, MAR07836, MAR07844, MAR11410, MAR11456, MAR11647, MAR11779	920
MAR05608, MAR05615, MAR05627, MAR05640, MAR05653, MAR05659, MAR05675, MAR05686, MAR05690, MAR05696, MAR05717, MAR05720, MAR05734, MAR05741, MAR05742, MAR05744, MAR05749, MAR05766, MAR05787, MAR05799, MAR05801, MAR05810, MAR05811, MAR05815, MAR05825, MAR05831, MAR05856, MAR05998	921

This PR focuses on the reactions that appears in 920 and 921 .