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[Gohelp] Gene Ontology microarray analysis

Midori Harris midori at ebi.ac.uk
Thu Nov 13 10:29:35 PST 2008


Dear Dr. Pandey,

Thank you for contacting the GO Consortium.

The AmiGO browser includes a tool, Term Enrichment, that you can use to 
analyze a list of gene products and look for term enrichment or clustering 
of annotation:

   http://amigo.geneontology.org/cgi-bin/amigo/term_enrichment

You must input a set of gene product identifiers -- UniProt or model 
organism database accessions -- for your query set and either (1) upload a 
set of gene product identifiers for your background/population set or (2) 
select a database filter to set your background annotation set for 
comparison. Should you choose this option, please let us know if you have 
any problems or further questions.

There are also a number of tools developed outside the GO Consortium, that 
you may be able to use to analyze your microarray results. We list these 
tools on the GO Tools web page:

   http://www.geneontology.org/GO.tools.shtml

You will probably be most interested in the microarray/proteomic tools 
section:

   http://www.geneontology.org/GO.tools.microarray.shtml

Of the many tools available, we have actually used only a few; some that 
have worked well for us are:

   Onto-Tools suite - http://vortex.cs.wayne.edu/
   g:profiler - http://biit.cs.ut.ee/gprofiler/index.cgi#qs
   FatiGO  - http://www.fatigo.org/

Please note that because all of these tools are developed outside the GO 
Consortium, you should contact the tool developers directly for 
assistance.

Regards,
Midori



> Date: Thu, 13 Nov 2008 10:18:27 -0600
>
> Hello,
>
> I have performed some gene microarray analysis and having a list of 1000
> genes. I like to categorize them according to their biological function
> (Gene Ontology). Can you please tell me some free software?
>
>
> Sincerely,
>
> Ravi S. Pandey, PhD
>
> Post-doctoral Fellow
>
> M533 Department of Medical Pharmacology & Physiology
> University of Missouri-School of Medicine
> Columbia, MO- 65212 USA
>
> Phone : 573-882-8435 (O)
>
>           : 515-451-7974 (M)
>



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