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Question: How to plot Gene Ontology categories
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gravatar for affy snp
10.3 years ago by
affy snp640
affy snp640 wrote:
Hi all, I recently came across a paper (Maria Chahrour, et al. MeCP2, a Key Contributor to Neurological Disease, Activates and Represses TranscriptionScience 320, 1224 (2008);) and am very interested in supplementary Figure S1 which basically plots cellular component, biological process, and molecular function categories that differ significantly based on on genes that are differentially expressed in two conditions. I wonder whether any R package or codes could achieve that task. Thanks much, Allen [[alternative HTML version deleted]]
ADD COMMENTlink modified 10.3 years ago by Stephen Henderson1.0k • written 10.3 years ago by affy snp640
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gravatar for Stephen Henderson
10.3 years ago by
Stephen Henderson1.0k wrote:
Hi The datasets here are from the MSigDB (C5: Gene Ontology GeneSets) http://www.broad.mit.edu/gsea/msigdb/index.jsp Software from the same site GSEA will do a similar analysis and give not a Z-value but what they call a 'normalised enrichment score' and an FDR cutoff for significant enrichments. Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Proc. Natl. Acad. Sci. USA 102, 15545-15550. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles An R package R-GSEA is available to do this. http://www.broad.mit.edu/gsea/downloads.jsp Stephen Henderson Cancer Institute, Paul O'Gorman Building Huntley Street, University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of ss Sent: 30 May 2008 02:19 To: BioC Subject: [BioC] How to plot Gene Ontology categories Hi all, I recently came across a paper (Maria Chahrour, et al. MeCP2, a Key Contributor to Neurological Disease, Activates and Represses TranscriptionScience 320, 1224 (2008);) and am very interested in supplementary Figure S1 which basically plots cellular component, biological process, and molecular function categories that differ significantly based on on genes that are differentially expressed in two conditions. I wonder whether any R package or codes could achieve that task. Thanks much, Allen [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ********************************************************************** This email and any files transmitted with it are confide...{{dropped:7}}
ADD COMMENTlink written 10.3 years ago by Stephen Henderson1.0k
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