[BioC] KEGG pathways gene list

Weiwei Shi helprhelp at gmail.com
Fri Apr 13 17:54:38 CEST 2007


As to your second question,

I am not sure if "linearity" exists for a pathway. In our research, we
created a "noodle" structure by hand but I assume KEGG pathway is a
network instead of a linear noodle. So you might need to sacrifice
your defn. of linear order or create noodles by yourself.

my2cents,

weiwei

On 4/13/07, Srinivas Iyyer <srini_iyyer_bio at yahoo.com> wrote:
> 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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-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III



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