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Bioinformatics Advance Access originally published online on February 5, 2004
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Bioinformatics 20(6) © Oxford University Press 2004; all rights reserved.

Applications Note

Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology

Peter N. Robinson 1,*, Andreas Wollstein 1, Ulrike Böhme 1 and Brad Beattie 2

1 Institute of Medical Genetics, Charité University Hospital, Humboldt University, Augustenburger Platz 1, 13353 Berlin, Germany and 2 Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Received on September 26, 2003 ; accepted on November 18, 2003
Advance Access Publication February 5, 2004

Summary: An XML-based Java application is described that provides a function-oriented overview of the results of cluster analysis of gene-expression microarray data based on Gene Ontology terms and associations. The application generates one HTML page with listings of the frequencies of explicit and implicit Gene Ontology annotations for each cluster, and separate, linked pages with listings of explicit annotations for each gene in a cluster.

Availability: http://www.charite.de/ch/medgen/ontologizer

Contact: peter.robinson{at}charite.de

* To whom correspondence should be addressed.


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