different IDs conversion to Gene ID/symbol

Question

[mrashad]

Dear all,

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?

Thanks

[Ram]

What have you tried? By the way, how does one map metabolites to genes?

[mrashad]

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.

[Ram]

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.

[DareDevil]

Provide the sample IDs.

What are KO IDs? Is it from KEGG?

[mrashad]

Kegg orthology ID, yes they are from KEGG.

Answer 1

[DareDevil]

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

[mrashad]

Thanks a lot for this fruitful answer

[Ram]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.