[BioC] GOstats - KEGG & PFAM mappings to Entrez ID

Sean Davis sdavis2 at mail.nih.gov
Wed Oct 15 14:05:30 CEST 2008

On Wed, Oct 15, 2008 at 7:53 AM, Tim Smith <tim_smith_666 at yahoo.com> wrote:
> Hi,
> I was using the hyperGTest in GOstats to find significant KEGG and PFAM terms. I have the entrez IDs of a set of genes and I test these with a universe of entrez IDs in hyperGTest to get the significant KEGG and PFAM terms. Now, I want to know which particular entrez IDs in my set of genes map to a particular significant KEGG/PFAM ID.
> I checked the KEGG.db (and PFAM.db) packages, but they don't have a KEGG ID to Entrez ID mapping. How can I get this? I guess GOstats is using a mapping of sorts in the hyperGTest, but where can I find it?

Look at the org.Hs.eg.db package (for human).  There are mappings there.


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