[BioC] How to quikly know whether two genes are in the same pathway or not?

[James F. Reid]

Hi Fabrice,

suppose you are using human genes and that you have gene symbols then 
you could do something like this:

library("org.Hs.eg.db")

twoGenes <- c("ATM", "TP53")
## convert them to Entrez Gene ids
twoGenesEG <- unlist(mget(twoGenes, org.Hs.egSYMBOL2EG))
twoGenesEGkegg <- mget(twoGenesEG, org.Hs.egPATH)
commonKegg <- intersect(twoGenesEGkegg[[1]], twoGenesEGkegg[[2]])
print(commonKegg)
##[1] "04110" "04115" "04210"
## what are these pathways
library("KEGG.db")
mget(commonKegg, KEGGPATHID2NAME)
##$`04110`
##[1] "Cell cycle"
##
##$`04115`
##[1] "p53 signaling pathway"
##
##$`04210`
##[1] "Apoptosis"

HTH,
J.



On 05/21/2011 01:39 PM, Fabrice Tourre wrote:
> If just using Gene symbol is OK or should convert Gene symbol to KEGG
> gene ids first?
>
>
>
> On Sat, May 21, 2011 at 12:58 PM, Fabrice Tourre<fabrice.ciup at gmail.com>  wrote:
>> Dear list,
>> Is there some packages can quikly know whether two genes are in the
>> same pathway or not? For example, kegg pathway.
>> Thanks.
>>
>
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