Hi January,

2011/2/28 January Weiner <january.weiner@mpiib-berlin.mpg.de>

> Dear all,
>
> my tool of choice currently is SPIA, a package that seems to provide
> sophisticated analysis of pathways (including both, gene set
> enrichment analysis and pathway perturbation analysis). I wonder what
> other tools you could recommend? The task at hand is to identify
> differentially regulated pathways given information on differentially
> expressed genes, using a solid, but broad pathway database.


The package DEGraph from bioconductor (
http://www.bioconductor.org/help/bioc-views/2.7/bioc/html/DEGraph.html)
allows you to test if the genes in a given network are differentially
expressed while taking the network structure into account.

See
http://www.bepress.com/cgi/viewcontent.cgi?article=1274&context=ucbbiostatfor
examples and more details on what exactly is tested (or feel free to
ask
me).

For the moment the package allows you to test any KEGG pathway. I'm working
on adding the NCI, Biocarta and Reactome networks.

Best,

Laurent

-- 
Laurent Jacob
Department of Statistics
UC Berkeley
http://cbio.ensmp.fr/~ljacob

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