Refine GPR in tryptophan metabolism pathway

[haowang-bioinfo]

gene	rxn	GPR	Manual check	GPT check if enzyme's substrates and products cover reaction's metabolites
ENSG00000137124	MAR00051	ENSG00000111275 or ENSG00000137124 or ENSG00000159423	GPR is match, GPT is right	Yes
ENSG00000111275	MAR00051	ENSG00000111275 or ENSG00000137124 or ENSG00000159423	GPR is match, GPT is right	Yes
ENSG00000159423	MAR00051	ENSG00000111275 or ENSG00000137124 or ENSG00000159423	GPR Not match, GPT is right. RHEA:30235	No
ENSG00000137124	MAR08563	ENSG00000111275 or ENSG00000137124 or ENSG00000164904	GPR is match, GPT is wrong	No
ENSG00000111275	MAR08563	ENSG00000111275 or ENSG00000137124 or ENSG00000164904	GPR is match, GPT is right	Yes
ENSG00000164904	MAR08563	ENSG00000111275 or ENSG00000137124 or ENSG00000164904	GPR is match, GPT is wrong	No
ENSG00000075239	MAR03885	ENSG00000075239	GPR is match, GPT is right	Yes
ENSG00000197448	MAR03124	ENSG00000008394 or ENSG00000100577 or ENSG00000197448	GPR is match, GPT is wrong	No
ENSG00000100577	MAR03124	ENSG00000008394 or ENSG00000100577 or ENSG00000197448	GPR is match, GPT is wrong	No
ENSG00000008394	MAR03124	ENSG00000008394 or ENSG00000100577 or ENSG00000197448	GPR is match, GPT is right	Yes
ENSG00000084754	MAR03164	ENSG00000084754 and ENSG00000113790 and ENSG00000127884	GPR is match, GPT is wrong	No
ENSG00000113790	MAR03164	ENSG00000084754 and ENSG00000113790 and ENSG00000127884	GPR is match, GPT is wrong (Peroxisome)	No
ENSG00000127884	MAR03164	ENSG00000084754 and ENSG00000113790 and ENSG00000127884	GPR is match, GPT is wrong	No
ENSG00000138796	MAR03166	ENSG00000072506 and ENSG00000084754 and ENSG00000138796	GPR is match, GPT is right	No
ENSG00000084754	MAR03166	ENSG00000072506 and ENSG00000084754 and ENSG00000138796	GPR is match, GPT is wrong	No
ENSG00000072506	MAR03166	ENSG00000072506 and ENSG00000084754 and ENSG00000138796	GPR is match, GPT is right	No
ENSG00000147576	MAR02858	ENSG00000147576	no supporting evidence	No
ENSG00000109576	MAR03048	ENSG00000109576	no supporting evidence	No
ENSG00000140465	MAR08566	ENSG00000138061 or ENSG00000140465 or ENSG00000140505 or ENSG00000165841	no supporting evidence	No
ENSG00000165841	MAR08566	ENSG00000138061 or ENSG00000140465 or ENSG00000140505 or ENSG00000165841	no supporting evidence	No
ENSG00000140505	MAR08566	ENSG00000138061 or ENSG00000140465 or ENSG00000140505 or ENSG00000165841	no supporting evidence	No
ENSG00000138061	MAR08566	ENSG00000138061 or ENSG00000140465 or ENSG00000140505 or ENSG00000165841	no supporting evidence	No
ENSG00000069535	MAR08092	ENSG00000069535 or ENSG00000189221	probably match	No
ENSG00000189221	MAR08092	ENSG00000069535 or ENSG00000189221	probably match	No
ENSG00000132437	MAR08091	ENSG00000132437	GPR Not match, GPT is right	No
ENSG00000109576	MAR08564	ENSG00000109576 or ENSG00000137944 or ENSG00000171097	GPR is match, GPT is wrong, missing water	No
ENSG00000109576	MAR02765	ENSG00000109576 or ENSG00000137944	GPR is match, GPT is wrong	No
ENSG00000137944	MAR08564	ENSG00000109576 or ENSG00000137944 or ENSG00000171097	GPR is match, GPT is wrong, missing water	No
ENSG00000137944	MAR02765	ENSG00000109576 or ENSG00000137944	GPR is match, GPT is wrong	No
ENSG00000171097	MAR08564	ENSG00000109576 or ENSG00000137944 or ENSG00000171097	GPR is match, GPT is wrong, missing water	No

[feiranl]

As for the no supporting evidence, I suggest we keep it for now without making changes?

[feiranl]

It would be great if there is a detailed list for how to change

[haowang-bioinfo]

yes, a detail list is coming

[haowang-bioinfo]

Action list based on manual inspection:

gene	rxn	GPT check if enzyme's substrates and products cover reaction's metabolites	Actions	Manual insepction
ENSG00000137124	MAR00051	Yes	No need to change
ENSG00000111275	MAR00051	Yes	No need to change
ENSG00000159423	MAR00051	No	remove ENSG00000159423 from MAR00051	do not supported by Uniprot
ENSG00000137124	MAR08563	No	keep it	supported by Uniprot annotiation
ENSG00000111275	MAR08563	Yes	No need to change
ENSG00000164904	MAR08563	No	keep it	supported by Uniprot annotiation
ENSG00000075239	MAR03885	Yes	No need to change
ENSG00000197448	MAR03124	No	keep it	largely supported by Uniprot
ENSG00000100577	MAR03124	No	keep it	largely supported by Uniprot
ENSG00000008394	MAR03124	Yes	No need to change
ENSG00000084754	MAR03164	No	keep it	supported by Uniprot annotiation
ENSG00000113790	MAR03164	No	remove, peroxisome source	keep it in peroxisome version MAR03103
ENSG00000127884	MAR03164	No	keep it	supported by Uniprot annotiation
ENSG00000138796	MAR03166	No	keep it	supported by Uniprot annotiation
ENSG00000084754	MAR03166	No	remove	do not supported by Uniprot
ENSG00000072506	MAR03166	No	keep it	supported by Uniprot annotiation
ENSG00000147576	MAR02858	No	keep it	No enough evidence to make change
ENSG00000109576	MAR03048	No	keep it	largely supported by Uniprot
ENSG00000140465	MAR08566	No	keep it	No enough evidence to make change
ENSG00000165841	MAR08566	No	keep it	No enough evidence to make change
ENSG00000140505	MAR08566	No	keep it	No enough evidence to make change
ENSG00000138061	MAR08566	No	keep it	No enough evidence to make change
ENSG00000069535	MAR08092	No	keep it	reaction should be in mitochondrion, now in cytosol
ENSG00000189221	MAR08092	No	keep it	reaction should be in mitochondrion, now in cytosol
ENSG00000132437	MAR08091	No	keep it	supported by other databases
ENSG00000109576	MAR02765	No	keep it, mitochondrion source	mito version, supported by Uniprot, match to Rhea: 65560
ENSG00000137944	MAR02765	No	keep it, in both mitochondrion and cytosol	mito version, supported by Uniprot, match to Rhea: 65560
ENSG00000171097	MAR08564	No	keep it, cytosol source	cytosol version, supported by Uniprot, match to Rhea: 65560
ENSG00000109576	MAR08564	No	remove, mitochondrion source	cytosol version, supported by Uniprot, match to Rhea: 65560
ENSG00000137944	MAR08564	No	keep it, in both mitochondrion and cytosol	cytosol version, supported by Uniprot, match to Rhea: 65560

[haowang-bioinfo]

Changes to GPRs of MAR03164 have been proposed in #634, will then be addressed elsewhere

[haowang-bioinfo]

fixed in #708