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remove non-metabolic gene from Phenylalanine, tyrosine and tryptophan biosynthesis #471
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Maybe there are still some of them are related to RNA modification rather than the amino acid synthesis. I can double check all of them. |
Since the reactions are methylations, a lot of the isozymes are probably different types of methyltransferases. So it is a bit similar to the issue of the generic phosphorylation reaction having all the kinases associated with it. Maybe only a subset of these actually catalyze the reactions involving these specific substrates, and the others could be removed, but I'm not sure. |
it does appear so - many are methyltransferases catalyzing other substrates than beta-carboline or salsolinol
sounds good, will also test with GPT model |
After GPT check and manual check, all genes are actually not associated with these two reactions.
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@feiranl nice results! Good correlation between manual curation and GPT curation could be observed. |
Both manual and GPT curations showed that all genes of There could be two follow-up implementation options:
Given their distribution as dead-end reactions in the network, I lean toward the option 1. |
The two reactions (MAR06710 and MAR06737) have identical GPRs and each has 72 genes, 65 of which just get involve in these two reactions.
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I believe we should get rid of these two reactions and their gene-protein-reaction associations. I was uncertain before because I was worried that if we got rid of too many reactions, it might become confusing if we want to add them back in the future. However, I now realize that even if we do decide to bring them back, we can still use the same reaction IDs, so it wouldn't be as complicated as I initially thought. So now I vote for remove. |
When in doubt, I would lean towards the answer supported by validation. |
Then I will remove those two rxns. |
Description of the issue:
Phenylalanine, tyrosine and tryptophan biosynthesis
:Current feature/value/output:
Expected feature/value/output:
I hereby confirm that I have:
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