different IDs conversion to Gene ID/symbol
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13 months ago
mrashad ▴ 60

Dears, 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

#multi_omics • 576 views
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What have you tried? By the way, how does one map metabolites to genes?

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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.

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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.

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Provide the sample IDs.

What are KO IDs? Is it from KEGG?

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Kegg orthology ID, yes they are from KEGG.

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13 months ago
dare_devil ★ 1.5k

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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Thanks a lot for this fruitful answer

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