looking for an expression analysis tool

[Cheng, Jill]

Hi Jane,
NetAFFX provides a free tool which allows user to import a gene list
(GB_ACC or probeset_names), and visualize it in the context of the GO
DAG.  The tool does Chi-square tests on all branches of the DAG, and
renders the GO DAG as a heat map where nodes are colored based on the
statistics, so the enriched branches can be visually identified.
The reference of the tool was published: 
NetAffx Gene Ontology Mining Tool: a visual approach for microarray data
analysis.
Bioinformatics. 2004 Jun 12;20(9):1462-3. Epub 2004 Feb 12. 
Jill 

-----Original Message-----
From: owner-gofriends at genome.stanford.edu
[mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Jane Lomax
Sent: Tuesday, June 13, 2006 7:24 AM
To: gofriends at genome.stanford.edu
Subject: looking for an expression analysis tool

Hi - does anyone devevelop, or know of, a gene expression analysis tool
that uses GO, and allows a user to upload their own gene association
file, preferably in standard GO format?

This is useful for species with no GO annotation in the GO database.

many thanks,

Jane

--
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

p: +44 1223 492516
f: +44 1223 494468

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