[BioC] How to plot Gene Ontology categories

[Stephen Henderson]

Hi

The datasets here are from the MSigDB (C5: Gene Ontology GeneSets)

http://www.broad.mit.edu/gsea/msigdb/index.jsp

Software from the same site GSEA will do a similar analysis and give not
a Z-value but what they call a 'normalised enrichment score' and an FDR
cutoff for significant enrichments. 

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L.,
Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E.
S. & Mesirov, J. P. (2005) Proc. Natl. Acad. Sci. USA 102, 15545-15550.
Gene set enrichment analysis: A knowledge-based approach for
interpreting genome-wide expression profiles

An R package R-GSEA is available to do this.

http://www.broad.mit.edu/gsea/downloads.jsp



Stephen Henderson
Cancer Institute, Paul O'Gorman Building
Huntley Street, University College London
United Kingdom, WC1E 6BT
+44 (0)207 679 6827
 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of ss
Sent: 30 May 2008 02:19
To: BioC
Subject: [BioC] How to plot Gene Ontology categories

Hi all,

I recently came across a paper (Maria Chahrour, et al.  MeCP2, a Key
Contributor to Neurological Disease,
Activates and Represses TranscriptionScience 320, 1224 (2008);) and am
very
interested in supplementary
Figure S1 which basically plots cellular component, biological process,
and
molecular function categories
that differ significantly based on on genes that are differentially
expressed in two conditions. I wonder whether
any R package or codes could achieve that task.

Thanks much,
     Allen

	[[alternative HTML version deleted]]

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