Remove PPARA Reactions

[Devlin-Moyer]

Main improvements in this PR:

As discussed in the comments on #580, removes all reactions involving MAM01268 or MAM02757 in all compartments:

• MAR00024
• MAR00025
• MAR00026
• MAR00027
• MAR00028
• MAR00029
• MAR05173
• MAR05289
• MAR13064

Also removes all metabolites that only participated in those reactions:

• MAM01816n
• MAM01268c
• MAM01268e
• MAM01268m
• MAM01268n
• MAM01268r
• MAM01268x
• MAM02757c
• MAM02757l
• MAM02757n

Also removes all genes that only participated in one or more of these reactions:

• ENSG00000069667
• ENSG00000101849
• ENSG00000118137
• ENSG00000126368
• ENSG00000135744
• ENSG00000137574
• ENSG00000139278
• ENSG00000140396
• ENSG00000141027
• ENSG00000142453
• ENSG00000143344
• ENSG00000158874
• ENSG00000166821
• ENSG00000167772
• ENSG00000169375
• ENSG00000170485
• ENSG00000171720
• ENSG00000177565
• ENSG00000186350
• ENSG00000186951
• ENSG00000196498
• ENSG00000198646

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

[Devlin-Moyer]

Apparently MAR00024 was the only reaction that MAM01816n participated in, so I'm also going to remove that

[haowang-bioinfo]

this is a natural follow-up implementation to the discussion in #580 - nice work @Devlin-Moyer

if to remove all reactions involving MAM01268, should MAR00030 be also be removed?

[Devlin-Moyer]

MAR00030 was removed by #657

[haowang-bioinfo]

these removed genes are mostly annotated with regulatory function. In particular, ENSG00000137574 and ENSG00000142453 are assigned with methyltransferase activity. Still they don't appear to be involved into any metabolic process.

it's okay to remove the genes in my view, and they can be added later once concrete evidence is provided