How to quikly know whether two genes are in the same pathway or not?
1
0
Entering edit mode
@fabrice-tourre-4394
Last seen 9.6 years ago
Dear list, Is there some packages can quikly know whether two genes are in the same pathway or not? For example, kegg pathway. Thanks.
• 819 views
ADD COMMENT
0
Entering edit mode
@fabrice-tourre-4394
Last seen 9.6 years ago
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. >
ADD COMMENT
0
Entering edit mode
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. >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLY

Login before adding your answer.

Traffic: 695 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6