[BioC] Which resources for pathway analysis?

[Gilbert Feng]

Hi, January

GeneAnswers integrates GO, DO, KEGG, and caBIO(NCI, Reactome and 
Biocarta) as well as gene interaction and entrez keywords search for 
gene set enrichment analysis. Finally, it can automatically generate a 
html report for one or multiple groups of gene set enrichment analysis 
with interactive networks.

Best

Gilbert



On 2/28/11 9:43 AM, January Weiner wrote:
> 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.
>
> There is, of course, a wide range of tools outside of R (e.g.
> PathVisio) which can be used for data mining and visualisation as well
> as running specific statistical analyses. I wonder what are you using
> in R.
>
> kind regards,
>
> j.
>