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

[Marc Carlson]

Sean Davis wrote:
> 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.
>
> Sean
>
> _______________________________________________
> 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
>
>   
Sean is right if you are working on human,  If you need information for
another species, you can look for a different "org.XX.eg.db" package
where "XX" is the 1st letters of the genus and species.  You can also
find this information inside of the chip based annotation packages.

  Marc