Dear Yuan, Per your request, Jianhong has added the function getEnrichedPATH in ChIPpeakAnno 2.3.3 (revision 63952 in dev repository). Please type help(getEnrichedPATH) for examples. Please let us know how it works out for you. Thanks for the great suggestions! Best regards, Julie On 3/12/12 1:58 PM, "Yuan Hao" <yuan.x.hao at="" gmail.com=""> wrote: > Hi Julie, > > I used to do GSEA and Hypergeometric test on GO or KEGG (R/ > Bioconductor "GOstats" , "GSEAlm" packages). KEGG seems the most > common database for pathways, but there are a couple of others (such > as those included in MsigDB) available. In terms of hypergeometric > test, the ideas behind either GO or KEGG are exactly the same. In the > later case, a single pathway is equivalent to a GO term. KEGG is a > collection of pathways and peaks from a ChIP-Seq experiment would > serve as selected genes. I attached a file contains pathways from > three databases retrieved from MsigDB, i.e. KEGG, BIOCARTA and > REACTOME. Thanks again for your reply! > > Regards, > Yuan > > > > > On 12 Mar 2012, at 00:38, Zhu, Lihua (Julie) wrote: > >> Dear Yuan, >> >> Thank you very much for your kind words! What kind of pathway are you >> looking for? If you could share your thoughts on the type of pathway >> analysis and give us a couple of examples or tools, we will see if >> we could >> add that to the package. >> >> Many thanks for sharing the great ideas! >> >> Best regards, >> >> Julie >> >> >> On 3/11/12 3:56 PM, "Yuan Hao" <yuan.x.hao at="" gmail.com=""> wrote: >> >>> Hi Julie, >>> >>> ChIPpeakAnno is a really powerful and user friendly package. Thanks >>> first for the great job! The package implemented hypergeometric test >>> on GO enrichment analysis. I am wondering would it be possible to >>> include the similar function on pathways? >>> >>> Regards, >>> Yuan >> >> > >

Dear Julie, Thanks a million for the prompt response! It's really efficient! I am recently hooked by some other types of data, and will give it a go when I get a chance. I believe it will benefit many others at the same time. Thanks again for both you and Jianhong! Cheers, Yuan On 15 Mar 2012, at 14:09, Zhu, Lihua (Julie) wrote: > Dear Yuan, > > Per your request, Jianhong has added the function getEnrichedPATH in > ChIPpeakAnno 2.3.3 (revision 63952 in dev repository). Please type > help(getEnrichedPATH) for examples. Please let us know how it works > out for > you. > > Thanks for the great suggestions! > > Best regards, > > Julie > > > On 3/12/12 1:58 PM, "Yuan Hao" <yuan.x.hao at="" gmail.com=""> wrote: > >> Hi Julie, >> >> I used to do GSEA and Hypergeometric test on GO or KEGG (R/ >> Bioconductor "GOstats" , "GSEAlm" packages). KEGG seems the most >> common database for pathways, but there are a couple of others (such >> as those included in MsigDB) available. In terms of hypergeometric >> test, the ideas behind either GO or KEGG are exactly the same. In the >> later case, a single pathway is equivalent to a GO term. KEGG is a >> collection of pathways and peaks from a ChIP-Seq experiment would >> serve as selected genes. I attached a file contains pathways from >> three databases retrieved from MsigDB, i.e. KEGG, BIOCARTA and >> REACTOME. Thanks again for your reply! >> >> Regards, >> Yuan >> >> >> >> >> On 12 Mar 2012, at 00:38, Zhu, Lihua (Julie) wrote: >> >>> Dear Yuan, >>> >>> Thank you very much for your kind words! What kind of pathway are >>> you >>> looking for? If you could share your thoughts on the type of pathway >>> analysis and give us a couple of examples or tools, we will see if >>> we could >>> add that to the package. >>> >>> Many thanks for sharing the great ideas! >>> >>> Best regards, >>> >>> Julie >>> >>> >>> On 3/11/12 3:56 PM, "Yuan Hao" <yuan.x.hao at="" gmail.com=""> wrote: >>> >>>> Hi Julie, >>>> >>>> ChIPpeakAnno is a really powerful and user friendly package. Thanks >>>> first for the great job! The package implemented hypergeometric >>>> test >>>> on GO enrichment analysis. I am wondering would it be possible to >>>> include the similar function on pathways? >>>> >>>> Regards, >>>> Yuan >>> >>> >> >> > >