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Bioinformatics Vol. 19 no. 18 2003
pages 2502-2504
© 2003 Oxford University Press

Applications Note

Characterizing gene sets with FuncAssociate

Gabriel F. Berriz 1, Oliver D. King 1, Barbara Bryant 2, Chris Sander 3 and Frederick P. Roth 1,*

1 Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, 250 Longwood Avenue, Boston, MA 02115, USA, 2 Millennium Pharmaceuticals, One Kendall Square, Cambridge, MA 02139, USA and 3 Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA

Received on April 2, 2003 ; revised on June 26, 2003 ; accepted on July 8, 2003

Summary: FuncAssociate is a web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment. Distinguishing features of FuncAssociate include the ability to handle ranked input lists, and a Monte Carlo simulation approach that is more appropriate to determine significance than other methods, such as Bonferroni or idák p-value correction. FuncAssociate currently supports 10 organisms (Vibrio cholerae, Shewanella oneidensis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Caenorhaebditis elegans, Drosophila melanogaster, Mus musculus, Rattus norvegicus and Homo sapiens).

Availability: FuncAssociate is freely accessible at http://llama.med.harvard.edu/Software.html. Source code (in Perl and C) is freely available to academic users ‘as is’.

Contact: fritz_roth{at}hms.harvard.edu

* To whom correspondence should be addressed.


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