UNIT 7.12 Using GenePattern for Gene Expression Analysis

  1. Heidi Kuehn,
  2. Arthur Liberzon,
  3. Michael Reich,
  4. Jill P. Mesirov

Published Online: 1 JUN 2008

DOI: 10.1002/0471250953.bi0712s22

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Kuehn, H., Liberzon, A., Reich, M. and Mesirov, J. P. 2008. Using GenePattern for Gene Expression Analysis. Current Protocols in Bioinformatics. 22:7.12:7.12.1–7.12.39.

Author Information

  1. Broad Institute of MIT and Harvard, Cambridge, Massachusetts

Publication History

  1. Published Online: 1 JUN 2008
  2. Published Print: JUN 2008


The abundance of genomic data now available in biomedical research has stimulated the development of sophisticated statistical methods for interpreting the data, and of special visualization tools for displaying the results in a concise and meaningful manner. However, biologists often find these methods and tools difficult to understand and use correctly. GenePattern is a freely available software package that addresses this issue by providing more than 100 analysis and visualization tools for genomic research in a comprehensive user-friendly environment for users at all levels of computational experience and sophistication. This unit demonstrates how to prepare and analyze microarray data in GenePattern. Curr. Protoc. Bioinform. 22:7.12.1–7.12.39. © 2008 by John Wiley & Sons, Inc.


  • GenePattern;
  • microarray data analysis;
  • workflow;
  • clustering;
  • classification;
  • differential;
  • expression analysis pipelines