retrieve human readable gene names from KEGG identifiers
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Osvaldo ▴ 40
@osvaldo-6150
Last seen 2.4 years ago
Spain

Dear Dr. Zhang,

I am starting to use your package KEGGgraph and I've got to a point where I cannot get the information I'd like to get. I've checked the KEGGgraph manual, but I was not able to find a description for that. I am pasting bellow a very small and simple example of what I mean, to try to explain it better.

The example is done with the Human Kegg pathway RAP1 signaling pathway (http://www.kegg.jp/kegg-bin/show_pathway?mmu04015+12801).
The graphical image of this patway in KEGG shows a node (GPCR receptor) where if you drop over the mouse pointer, you are able to see that there are two related entries, 12801-Cnr1 and 13489-Drd2. What I am able to get with KEGGgraph are the entry IDs 12801 and 13489, but what I would like to get are the associated gene names (Cnr1 and Drd2).

I did the following:

library(KEGGgraph)
tmp <- tempfile()
retrieveKGML(pathwayid='mmu04015' , organism='mmu' , destfile=tmp, method="wget")
pathway <- parseKGML(tmp)

nodes[[60]]@name[[1]] ---> retrieves mmu:12801
nodes[[60]]@name[[1]] ---> retrieves mmu:13489
 

So, is there a way to jump from this numerical id names to the corresponding Cnr1 and Drd2 gene names?
 

Thanks very much in advance.

kegggraph • 2.3k views
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@zhang-jitao-david-5737
Last seen 2.6 years ago
Switzerland

Dear Osvaldo,

   Thank you for using KEGGgraph.

   The identifier (mmu:12801) is composed of species (mmu) and Entrez Gene ID (12801). So strsplit will do the trick to get EntrezGeneID

   From GeneID to gene symbos one can choose many ways. One of them is biomaRt

   Best wishes,

David

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Robert Castelo ★ 2.9k
@rcastelo
Last seen 11 days ago
Barcelona/Universitat Pompeu Fabra

I think you should also check out the function translateKEGGID2GeneID() from the KEGGgraph package.

cheers,

robert.

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Osvaldo ▴ 40
@osvaldo-6150
Last seen 2.4 years ago
Spain

Thanks very much for your quick answers !!

I will try biomaRt.

Robert, I've already tried the function 'translateKEGGID2GeneID', it provides the gene number ID (it simply removes mmu in this case).

translateKEGGID2GeneID("mmu:12801")
[1] "12801"

 

 

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@zhang-jitao-david-5737
Last seen 2.6 years ago
Switzerland

I am glad that you digged out translateKEGGID2GeneID:)

Have fun, David

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Osvaldo ▴ 40
@osvaldo-6150
Last seen 2.4 years ago
Spain

hi there again !

Although I haven't used the biomaRt package finally, it was a good hint to get to the 'rentrez' R package. I've done it this way:

library(rentrez)
entrez_summary(db="gene", id="12801")$name
[1] "Cnr1"
entrez_summary(db="gene", id="13489")$name
[1] "Drd2"
> entrez_summary(db="gene", id="13489")

 

or what is the same in my R script:

entrez_summary(db="gene", id=translateKEGGID2GeneID(nodes[[60]]@name[[1]]))$name
[1] "Cnr1"

entrez_summary(db="gene", id=translateKEGGID2GeneID(nodes[[60]]@name[[2]]))$name

[1] "Drd2"

 

thanks once more !!

osvaldo.

 

 

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