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 S̆idák 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’.

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Author notes

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