[BioC] KEGG: gene ids for nodes in a pathway

Saroj K Mohapatra saroj at vt.edu
Mon May 4 21:19:57 CEST 2009

Hello Tim:

To get all the entrez gene ids in a pathway ("04630")" in a variable 
called egs:

 > egs = get("04630", revmap(org.Hs.egPATH))

Then get the gene symbols for each gene ids:

 > syms = unlist(mget(egs, org.Hs.egSYMBOL))

Which of these gene symbols contain STAT?

 > syms[grep("STAT", syms)]
    6772     6773     6774     6775     6776     6777     6778
 "STAT1"  "STAT2"  "STAT3"  "STAT4" "STAT5A" "STAT5B"  "STAT6"

Best wishes,


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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