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=ucbbio statfor 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 [[alternative HTML version deleted]]

Dear Gilbert, thanks for pointing me to GeneAnswers, this is definitely an interesting tool. I have installed GeneAnswers using biocLIte. However, in the documentation, I do find GO, DOLite and KEGG mentioned, but not caBIO. How do I use GeneAnswers with caBIO? Kind regards, j. > sessionInfo() R version 2.10.1 (2009-12-14) i486-pc-linux-gnu locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GeneAnswers_1.2.0 MASS_7.3-5 RSQLite_0.9-1 [4] DBI_0.2-5 XML_3.1-0 annotate_1.24.1 [7] AnnotationDbi_1.8.2 Biobase_2.6.1 RCurl_1.4-2 [10] bitops_1.0-4.1 igraph_0.5.5-1 loaded via a namespace (and not attached): [1] tools_2.10.1 xtable_1.5-6 On Mon, Feb 28, 2011 at 4:49 PM, Gilbert Feng <g-feng at="" northwestern.edu=""> wrote: > 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. >> > > -- -------- 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