Hi, Regarding Pathway analysis: In bioconductor when I load: library(KEGG) I can do this: kegg <- as.list(rae230aPATH2PROBE); and I can generate heatmap of pathway probes which are involved in my DEgenes so, I can see which genes are up and down in perticular pathway. how can I use interaction data extracted from human BioCarta pathways for my differentially expressed genes? if anyone has done please let me know... Thank you, Saurin -- |------------------------------------------------ | Saurin Jani | Bioinformatician | | Department of Cell Biology and Anatomy | Medical University of South Carolina (MUSC) | 173 Ashley Ave | Charleston,SC - 29407 (US) | | Email: jani@musc.edu | Phone: (843)792-5483 |------------------------------------------------ Quoting Robert Gentleman <rgentlem@fhcrc.org>: > There is a KEGG package, and we also have KEGGSOAP that give you access > to the KEGG data (for non-commercial use, if I recall correctly). You > can supplement this with the graph package, RBGL and Rgraphviz to do > most of the pathway stuff you want to. > > Another option is to make use of the CMAP data, which is potentially > more interesting because it has the pathways already represented as a > graph. But it is also more work as we have not managed to build any > interfaces for this (they have some though); > the url is http://cmap.nci.nih.gov/PW > > Robert > > On Dec 16, 2004, at 3:11 PM, Josephine Liang wrote: > > > Hi, fellow bioconductor members; > > > > In my memory, there is a vague rememberance that this is a package in > > Bioconductor called Pathway, I went to Bioconductor site , could not > > find a package named pathway in release 1.5, did I remember it wrong? > > Or the package is in an older release? If it is, which release it is? > > how do I access it? > > > > Thanks for all your help in advance > > > > Josephine > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > +------------------------------------------------------------------- ---- > ----------------+ > | Robert Gentleman phone: (206) 667-7700 > | > | Head, Program in Computational Biology fax: (206) 667-1319 | > | Division of Public Health Sciences office: M2-B865 > | > | Fred Hutchinson Cancer Research Center > | > | email: rgentlem@fhcrc.org > | > +------------------------------------------------------------------- ---- > ----------------+ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >