KEGGREST mapping between genes and pathways
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@zhangjianhai-12955
Last seen 4.2 years ago

Hello,

I want to enrich KEGG pathways on my rice genes. I tried "clusterProfiler", but its input is entrezID and my gene ids are RAPIDs (Os02g0617800). I want to keep using the RAPIDs, so I have to write my own enrichment functions. To do this, I need the mapping between RAPIDs and pathways. How to get the mapping from KEGGRSET?

Regards.

keggrest mapping genes to pathways • 1.9k views
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@gordon-smyth
Last seen 32 minutes ago
WEHI, Melbourne, Australia

You don't need to convert your IDs. KEGG already provides a mapping between the Japanese rice genome pathways and RAPIDs.

For example, you can use the kegga function in the limma package with species.KEGG="dosa" and it will use RAPIDs directly. To see which RAPIDs KEGG is using, have a look at the gene to pathway annotation:

> library(limma)
> GK <- getGeneKEGGLinks(species.KEGG="dosa")
> head(GK)
           GeneID      PathwayID
1 Os01t0118000-01 path:dosa00010
2 Os01t0147900-01 path:dosa00010
3 Os01t0160100-01 path:dosa00010
4 Os01t0190400-01 path:dosa00010
5 Os01t0191700-01 path:dosa00010
6 Os01t0276700-01 path:dosa00010

Alternatively, to get NCBI Entrez Gene IDs instead:

> GK.Entrez <- getGeneKEGGLinks(species.KEGG="osa")
> head(GK.Entrez)
     GeneID     PathwayID
1 107275630 path:osa00010
2 107277365 path:osa00010
3   4324066 path:osa00010
4   4324263 path:osa00010
5   4324666 path:osa00010
6   4325027 path:osa00010
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It is very useful, but why there is "-01" or "-00" at the end of gene IDs (e.g. Os01t0191700-01)?

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You'd have to ask KEGG rather than me. Presumably they are transcript version numbers. It might be fine to remove them.

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I see. Thank you very much for reply!

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All the gene ids have a "t" (Os01t0118000) inside rather than a "g" (Os05g0532600). Why is that?

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The ID with "t" is the transcript ID. The ID with "g" is the locus ID. See for example the gene annotation file you can download from here:

https://rapdb.dna.affrc.go.jp/download/irgsp1.html

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I am working on locus IDs, to convert transcript ids to locus ids, should I replace "t" with "g" (based on your link, it seems yes)?

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It seems 50 transcript ids resulting from "getGeneKEGGLinks" are not present int the link you shared. Do you know the source of transcript IDs in "limma"?

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