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. -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web?? : www.mpiib-berlin.mpg.de Tel? ?? : +49-30-28460514

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. >