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GenePattern is a powerful genomic analysis platform that provides access to more than 125 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.


Getting Started

quickstartLearn to use GenePattern in 10 minutes:
Learn hands-on with the Quick Start tutorial
Learn by watching short video tutorials
onlineRun analyses now at Broad server
Use GenePattern to run analyses on a server at the Broad Institute.
download Download GenePattern
GenePattern runs on Windows, Mac, and Linux.

Modules from Recent Publications


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What's New

8/4/2010: ConvertToMAGETAB has been released. The module exports microarray data from GenePattern in MAGE-TAB format.

6/30/2010: GenePattern 3.2.3 is now available. Run analyses on the Broad server or download GenePattern. For more information, see the release notes.

6/18/2010: MAGETABImportViewer has been released. The module imports data in MAGE-TAB format into the GenePattern .gct or .cls file formats.

3/22/2010: CBS (Circular Binary Segmentation) has been released. The module segments copy number data using the methodology described in Olshen et. al., 2004.

1/22/2010: The Microsoft® Word 2007 add-in for the GenePattern Reproducible Research Document (GRRD) is now available. Mesirov (Science, 327:415, 2010) mentions the add-in in a Policy Forum discussing the importance of making reproducibility easily accessible to nonprogramming users in the context of scientific manuscripts.

Citing GenePattern
Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501
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National Cancer Institute NIGMS

Funded by the National Cancer Institute and the National Institute of General Medical Sciences.

GenomeSpace GenePattern is participating in the GenomeSpace initiative.

caBig Member of the caBIG™ Molecular Analysis Tools Knowledge Center.

best practices award Winner of the Editor's Choice award for the 2005 BioIT World Best Practices competition.