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fix: refine reactions, reversibility, and GPRs of Isocitrate Dehydrogenase metabolism #525
Conversation
- remove rxns: MAR04111, MAR04112, MAR04113, MAR04585, MAR04586, MAR04587, MAR04588 - modify GPRs for MAR0710, MAR0712, MAR03957, MAR03958
@Devlin-Moyer please review the changes made to Isocitrate Dehydrogenase reactions based on your proposal. |
@feiranl maybe you can double check this |
These commits are not fully documented in the #523 such as MAR03957 removal, and the proposed changes remain such as
@haowang-bioinfo could you explain it a little bit? Actually, I am not a fan of removing the multi-step reactions, since it may affect the flux distribution. For example in the mentioned loop |
all but two of the other reactions that cis-aconitate can participate in are transport reactions catalyzed by SLC25A1, and all of those reactions have an otherwise equivalent version that uses citrate or isocitrate in place of cis-aconitate, so removing the only sources of cis-aconitate aside from its exchange reaction would probably have no real impact on predicted/possible flux distributions
the only reactions involving cis-aconitate not on this table are the two steps of the reaction catalyzed by aconitase mentioned above (MAR04458 and MAR04589), the exchange reaction (MAR11350), and symport of cis-aconitate and sodium across the cell membrane (MAR099287) |
these commits didn't remove MAR03957, and the removal here includes only 7 reactions that are: MAR04111, MAR04112, MAR04113, MAR04585, MAR04586, MAR04587, MAR04588 (this is stated in the first point of PR message)
this PR didn't touch MAR04456, MAR04458, or MAR04589. |
Regarding the case of with the very nice table prepared by @Devlin-Moyer, it seems that the low resolution option is simple and good enough, according to Occam's razor principle here's one additional piece of evidence that reports mitochondrial TCA transporter Mtt1 that can relocate cis-aconitate from mitochondrion to cytosol |
for resolving the duplication of
what do you think? @Devlin-Moyer @feiranl |
Sounds good to me |
okay, implemented in 8e4f2d2 |
I found after this PR, there are three metabolites |
Good spot! you are absolutely right about the three orphan metabolites (MAM02662c, MAM02662m, MAM02662x) that currently do not involve into any reactions. |
now implemented in #556 |
This PR improves GPRs of isocitrate dehydrogenase reactions, as proposed by #523:
ENSG00000138413
: for MAR0710, MAR0712,ENSG00000182054
: for MAR03958ENSG00000067829 and ENSG00000101365 and ENSG00000166411
: for MAR03957I hereby confirm that I have:
develop
as a target branch