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
>
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