I have a group of KO IDs and metabolites HMDB ID needed to be changed to Gene IDs/symbols, Is there a suitable tool to convert them ?
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 biomaRt and org.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.
You can use data from here
$ wget -O KO.txt "http://rest.kegg.jp/list/ko"
$ head -n5 KO.txt
ko:K00001 E188.8.131.52, adh; alcohol dehydrogenase [EC:184.108.40.206]
ko:K00002 AKR1A1, adh; alcohol dehydrogenase (NADP+) [EC:220.127.116.11]
ko:K00003 hom; homoserine dehydrogenase [EC:18.104.22.168]
ko:K00004 BDH, butB; (R,R)-butanediol dehydrogenase / meso-butanediol dehydrogenase / diacetyl reductase [EC:22.214.171.124 1.1.1.- 126.96.36.1993]
ko:K00005 gldA; glycerol dehydrogenase [EC:188.8.131.52]
$ grep 'K22938' KO.txt
ko:K22938 SDCCAG3, ENTR1; serologically defined colon cancer antigen 3
You can also use KEGG Mapper
Thanks a lot for this fruitful answer
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