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Bioinformatics Advance Access originally published online on February 5, 2004
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Bioinformatics 20(7) © Oxford University Press 2004; all rights reserved.

Applications Note

CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology

N.H. Shah * and N.V. Fedoroff

The Huck Institute of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA

Received on May 29, 2003; revised on September 29, 2003; accepted on November 5, 2003
Advance Access Publication February 5, 2004

Summary: Analysis of microarray data most often produces lists of genes with similar expression patterns, which are then subdivided into functional categories for biological interpretation. Such functional categorization is most commonly accomplished using Gene Ontology (GO) categories. Although there are several programs that identify and analyze functional categories for human, mouse and yeast genes, none of them accept Arabidopsis thaliana data. In order to address this need for A.thaliana community, we have developed a program that retrieves GO annotations for A.thaliana genes and performs functional category analysis for lists of genes selected by the user.

Availability: http://www.personal.psu.edu/nhs109/Clench

Contact: nigam{at}psu.edu

* To whom correspondence should be addressed.


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