refine GPR for lactate dehydrogenase

[feiranl]

Description of the issue:

Enzyme	localization
ENSG00000134333	cytosol
ENSG00000166800	cytosol
ENSG00000111716	cytosol,mitochondria
ENSG00000171989	cytosol,mitochondira,nucleus
ENSG00000166796	cytosol
ENSG00000151116	extracellular

We may need to modify the GPR for rxn:

remove ENSG00000134333 from Peroxisome MAR04281 and mitochondria MAR04280 remove ENSG00000166800 from Peroxisome MAR04281 and mitochondria MAR04280 remove ENSG00000111716 from Peroxisome MAR04281 remove ENSG00000166796 from Peroxisome MAR04281 and mitochondria MAR04280 remove ENSG00000151116 from Peroxisome MAR04281 and mitochondria MAR04280 After removal, the rxn MAR04281 contain no gene association, not sure which gene to keep.

[haowang-bioinfo]

After removal, the rxn MAR04281 contain no gene association, not sure which gene to keep.

what do you think about MAR04281, delete it or keep with blank GPR?

remove ENSG00000151116 from Peroxisome MAR04281 and mitochondria MAR04280

only remove ENSG00000151116 from the 2 rxns or delete it from model?

[feiranl]

The ENSG00000151116 are responsible for the cytosol reaction, so we don't have to delete it from the model. Now as for the MAR04281, ENSG00000171989 was kept, since it is the most versatile one.

[haowang-bioinfo]

for the MAR04281, ENSG00000171989 was kept, since it is the most versatile one.

okay

The ENSG00000151116 are responsible for the cytosol reaction

Despite of annotated with lactate/malate dehyrogenase domain, the function of ENSG00000151116 is vaguely determined.

[feiranl]

Oh, do you think we should delete it?

[haowang-bioinfo]

Oh, do you think we should delete it?

good question, basically I think every change should be made based on some evidence, such as literature, experimental results, and manual reasoning. In this case, function of ENSG00000151116 was annotated as regulaor.

Ah just found that it had been deleted in #443 (Met Atlas has not synced with v1.14) - so decision was already made!