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Bioinformatics Advance Access originally published online on June 16, 2004
Bioinformatics 2004 20(17):3266-3269; doi:10.1093/bioinformatics/bth362
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Bioinformatics vol. 20 issue 17 © Oxford University Press 2004; all rights reserved.

Applications Note

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

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

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

Received on January 20, 2004; revised on May 3, 2004; accepted on June 4, 2004
Advance Access Publication June 17, 2004

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 plug-in are available for GeneSpring 5.0.2 and GeneSpring 6.1.1, and have been tested under Windows XP.

Contact: eugen_buehler{at}merck.com

* To whom correspondence should be addressed.

{dagger} These authors contributed equally to this work.


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