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GO question

Gavin Sherlock sherlock at genome.Stanford.EDU
Fri Jun 25 05:56:33 PDT 2004


Hi Antony,

I would be remiss if I didn't add my two cents to advertise 
GO::TermFinder (http://search.cpan.org/dist/GO-TermFinder/) which is an 
open source tool for calculating the significance of GO terms 
associated with a list of genes, using both p-values and False 
Discovery Rate.  It also creates browsable graphic output for you, and 
can be run in batch mode.  On a good day it will also make cups of tea 
and write your manuscripts for you as well :-)

Cheers,
Gavin
________________________________________________________

Gavin Sherlock
Assistant Professor, Research
Dept. of Genetics
Center for Clinical Sciences Research
269 Campus Drive,
Room 2255b,
Stanford,
CA 94305-5120
Tel: 650 498 6012
Fax: 650 724 3701

On Jun 24, 2004, at 4:09 PM, Antony Rodriguez wrote:

> Dear GO members,
>
> I came accross the GO website and wanted to ask you guys a specific 
> question.
>
> I have a small set of genes from humans (approx 200) and I retrieved 
> biological processes and molecular functions for each one.  My 
> question is, how or where do I go to compare the frequency 
> (abundances) for each category within this group with that of the 
> entire genome as a whole?  For instance if in this set there are 20 
> out of 200 genes with a 'transport' GO:0006810 biological process and 
> I wanted to determine if this is unusually high fraction within my 
> sample size as compared to the total fraction of 'transport' genes in 
> the entire human genome where would I search for such information?
>
> Thanks for the help,
>
> Antony Rodriguez, Ph.D.
> Fellow
> Mouse Genomics Team 82
> Wellcome Trust Sanger Institute
> Genome Campus
> Cambridge CB10 1SA  UK
> tel: 44-1223-834244 Ext: 7165
> FED EX ACCT: 1650 94344
>
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