Are there tools available for differential gene set analysis? e.g., if I apply the same treatment to two different cell lines, and find gene sets that are enriched in each with respect to untreated, can I compare the lists of gene sets and find ones that are significantly enriched in one but not the other?

If I understand your question correctly, Gostats and topGO in Bioconductor. Also DAVID http://david.abcc.ncifcrf.gov/ is an easy to use web based tool. Paul. On Tue, Apr 17, 2012 at 10:45 PM, Ed Siefker <ebs15242@gmail.com> wrote: > Are there tools available for differential gene set analysis? > > e.g., if I apply the same treatment to two different cell lines, > and find gene sets that are enriched in each with respect > to untreated, can I compare the lists of gene sets and > find ones that are significantly enriched in one but not > the other? > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com [[alternative HTML version deleted]]

Hi Ed, On 04/17/2012 11:45 PM, Ed Siefker wrote: > Are there tools available for differential gene set analysis? > > e.g., if I apply the same treatment to two different cell lines, > and find gene sets that are enriched in each with respect > to untreated, can I compare the lists of gene sets and > find ones that are significantly enriched in one but not > the other? Why don't you do it the other way round: First find genes that react differently to treatment in cell line 1 than in cell line 2. The do an enrichment analysis for these genes. To find these genes, do a GLM-based analysis testing for interactions between cell line and treatment, e.g., with DESeq. Simon

Dear Ed, Quite a few tools, for example: library(limma) ?roast ?camera ?romer Also for R-based gene sets: http://bioinf.wehi.edu.au/software/MSigDB/ Best wishes Gordon > Date: Tue, 17 Apr 2012 16:45:10 -0500 > From: Ed Siefker <ebs15242 at="" gmail.com=""> > To: bioconductor <bioconductor at="" r-project.org=""> > Subject: [BioC] differential gene set analysis > > Are there tools available for differential gene set analysis? > > e.g., if I apply the same treatment to two different cell lines, > and find gene sets that are enriched in each with respect > to untreated, can I compare the lists of gene sets and > find ones that are significantly enriched in one but not > the other? ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}