Hi Mark & Saroj,

Thanks for the replies.

As Saroj suggested, I could use grep to get to 'STAT1', 'STAT3',....etc. for the STAT pathway. However, I would like to automate the process for the pathway (and possibly several pathways). With grep, I would need to actually look at the pathway in KEGG, figure out the nodes (e.g. 'STAT', 'JAK', 'PI3K'...etc) and then perform a grep for each of these to get to the genes (e.g. 'STAT1', 'STAT3', ...etc. for the 'STAT' node) associated with each of these nodes. What I was looking for was something I could use so that I could automate the process. I guess I could still use grep if there was some way of getting to all the node labels ('STAT') in a particular pathway. Is there such functionality?

thanks again!






________________________________
From: Marc Carlson <mcarlson@fhcrc.org>

Cc: bioc <bioconductor@stat.math.ethz.ch>
Sent: Monday, May 4, 2009 6:05:52 PM
Subject: Re: [BioC] KEGG: gene ids for nodes in a pathway

Hi Tim,

I think that the mapping you are using below already maps the entrez
gene IDs associated with a particular pathway.  All you need to do is
use mget() instead of toTable().

So for pathway "04630", you can just get the associated entrez gene IDs
like this:

library(org.Hs.eg.db)
mget("04630", revmap(org.Hs.egPATH), ifnotfound=NA)


  Marc





Tim Smith wrote:
> Hi,
>
> I wanted a list of genes for a particular pathway arranged nodewise. For example, if I select the Jak-stat pathway ("http://www.genome.jp/kegg/pathway/hsa/hsa04630.html"), how do I get the entrez ids of genes associated with the node 'STAT' ? Currently, I use the following code:
>
> x <- toTable(org.Hs.egPATH)
>
> and then select genes associated with a particular pathway (e.g. for Jak-stat: "04630") . But this gives the entire set of genes associated with the pathway. Is there a way to get the entrez ids of the genes associated with each of the nodes ('JAK', 'STAT', 'STAM','PIAS' etc.) in the pathway?
>
> thanks!
>
>
>
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