Hi everyone, I am running differential gene (DE) expression analysis using RNA-seq data and I have used GOseq to find enriched Gene Ontology (GO) categories in the DE genes list. I have a couple of questions to ask, and hope someone can help me: Can I extract the number of genes, and IDs present in each enriched category using GOseq? If not, I suppose it is better to annotate all the genes for GO and find out which genes are annotated in a particular category. Is there a R-package that you would recommend to annotate genes using ENSEMBL and NCBI gene_IDs? Thanks, Fernando

Hi Fernando, The information you're after is not automatically returned as part of a normal GOseq analysis, but can be accessed pretty easily. The getgo function will return the mapping between GO categories and gene identifiers. The mapping from GO categories to genes can then be obtained by running the internal function reversemapping on the result. You can then look at your enriched mappings, which should be a subset of the above. For example, using the example data... library(goseq) data(genes) genes2go=getgo(names(genes),'hg19','ensGene') go2genes=goseq:::reversemapping(genes2go) More information about specific GO categories is available from the gene ontology website http://www.geneontology.org/ Cheers, Matt On 05/03/2011, at 4:31 AM, Biase, Fernando wrote: > Hi everyone, > > I am running differential gene (DE) expression analysis using RNA- > seq data and I have used GOseq to find enriched Gene Ontology (GO) > categories in the DE genes list. > I have a couple of questions to ask, and hope someone can help me: > > Can I extract the number of genes, and IDs present in each enriched > category using GOseq? > > If not, I suppose it is better to annotate all the genes for GO and > find out which genes are annotated in a particular category. Is > there a R-package that you would recommend to annotate genes using > ENSEMBL and NCBI gene_IDs? > > Thanks, > Fernando > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}