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Quoting Yogi Sundaravadanam <yogi.sundaravadanam at="" agrf.org.au="">: > > > Hi all > > > > I was wondering if anyone would please help me with this. > > > > I have a set of differentially expressed genes that I am interested in > and I want to find the GO ontologies they are associated with. Is there > a way I would be able to do this in any bioconductor package? I?d be > very grateful for this > > > > Thanks > > Yogi > > > > > > > > [[alternative HTML version deleted]] > > It sounds like you want to map some gene IDs to the corresponding GO ontology terms. For that you could use the GO pkg. http://bioconductor.org/packages/2.0/data/annotation/html/GO.html Marc

"Yogi Sundaravadanam" <yogi.sundaravadanam at="" agrf.org.au=""> writes: > I have a set of differentially expressed genes that I am interested in > and I want to find the GO ontologies they are associated with. Is there > a way I would be able to do this in any bioconductor package? Id be > very grateful for this There are a number of packages that can do things along these lines. You might look at GOstats (perhaps start with the vignette) and also look at: http://bioconductor.org/packages/2.0/GO.html + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/

Hi Yogi, Yogi Sundaravadanam wrote: > > > Hi all > > > > I was wondering if anyone would please help me with this. > > > > I have a set of differentially expressed genes that I am interested in > and I want to find the GO ontologies they are associated with. Is there > a way I would be able to do this in any bioconductor package? I?d be > very grateful for this That question is pretty ambiguous, and I can think of several answers that might be applicable. Are you asking: a.) Given a set of genes, I want to know the GO terms associated with each. b.) Given a set of genes, I want to know if there are any GO terms that are over-represented. c.) Given a set of genes, I want to know what GO ontologies the genes map to. d.) Something else? Can you re-specify your question to be a bit less ambiguous? Best, Jim > > > > Thanks > > Yogi > > > > > > > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623