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Bioinformatics Advance Access published online on June 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth362
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received January 20, 2004
Revised May 3, 2004
Accepted June 4, 2004

Applications note

The CRASSS plug-in for integrating annotation data with hierarchical clustering results

Eugen C. Buehler 1*, Jeffrey R. Sachs 1, Kui Shao 1, Ansuman Bagchi 1, Lyle H. Ungar 2

1 Applied Computer Science and Mathematics, Merck Research Laboratories, P.O. Box 2000 RY84-202, Rahway, NJ 07065-0900
2 Department of Computer & Information Science, University of Pennsylvania, 200 South 33rd Street, Philadelphia, PA 19104-6389

* To whom correspondence should be addressed. E-mail: eugen_buehler{at}merck.com.


  Abstract

Summary: We describe an algorithm for finding the most statistically significant non-overlapping subtrees of a hierarchical clustering of gene expression data with respect to a set of secondary data labels on genes. The method is implemented as a Java plug-in for a commercial gene expression analysis program (GeneSpring).

Availability: The JAR (Java Archive) file needed to use this plug-in and instructions on its installation and use can be obtained from http://www.cis.upenn.edu/~buehler/CRASSS.html. Versions of this plugin are available for GeneSpring 5.0.2 and GeneSpring 6.1.1, and have been tested under Windows XP.


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