[BioC] KEGG pathways gene list

Srinivas Iyyer srini_iyyer_bio at yahoo.com
Fri Apr 13 16:38:32 CEST 2007


Dear group, 
I have 2 questions to ask:

Question 1:
Give a pathway name for KEGG, how do I get all the
genes involved in that pathway.

>library(KEGG)
>wnt <- get("04310", KEGGPATHID2NAME)

 now how do I get gene names in wnt pathway. Here I am
not interested in taking say HGU133a chip and map all
probeset ids to wnt.  I just need genes in wnt. 


Question 2:
I have a vector of gene names as object 'mygenes'. 
I want to see if any genes in 'mygenes' are connected
in wnt pathway. 

mygenes <- c("Wnt","FZD10","DVL1","p53","Ras")

We know that Wnt,FZD10 and DVL1 are in linear order. 

Now is there any way to get the genes that are
connected. from mygenes, I want to get Wnt, FZD10 and
DVL1 are connected in order. Is this possible?

Please help me 
Thanks
Sri



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