different IDs conversion to Gene ID/symbol
1 answer
You can use data from here
$ wget -O KO.txt "http://rest.kegg.jp/list/ko"
$ head -n5 KO.txt
ko:K00001 E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]
ko:K00002 AKR1A1, adh; alcohol dehydrogenase (NADP+) [EC:1.1.1.2]
ko:K00003 hom; homoserine dehydrogenase [EC:1.1.1.3]
ko:K00004 BDH, butB; (R,R)-butanediol dehydrogenase / meso-butanediol dehydrogenase / diacetyl reductase [EC:1.1.1.4 1.1.1.- 1.1.1.303]
ko:K00005 gldA; glycerol dehydrogenase [EC:1.1.1.6]
$ grep 'K22938' KO.txt
ko:K22938 SDCCAG3, ENTR1; serologically defined colon cancer antigen 3
You can also use KEGG Mapper
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What have you tried? By the way, how does one map metabolites to genes?
There is R package called clusterprofiler get the pathways of Genes that out of clusters but the input of this package is gene ID, and I have genes and metabolites out of cluster not genes only for that I asked is there a way to convert the metabolites to genes or not.
Logically, metabolites are small chemical molecules while genes are stretches of functional DNA, so I don't think it makes sense to "map" genes to metabolites.
Like dare_devil says, samples of what you have and what you need would be useful. On a side note, explore packages like
biomaRtandorg.Hs.eg.db- these are helpful in mapping gene symbols, names and aliases.Provide the sample IDs.
What are KO IDs? Is it from KEGG?
Kegg orthology ID, yes they are from KEGG.