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Characterizing gene sets with FuncAssociate.

Gabriel F Berriz·Oliver D King·Barbara Bryant·Chris Sander·Frederick P Roth
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Abstract

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'.

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AlgorithmsAnimalsDatabase Management SystemsDatabases, ProteinGene Expression ProfilingInformation Storage and RetrievalNatural Language ProcessingProteinsRatsReproducibility of ResultsSensitivity and SpecificitySequence Analysis, ProteinSoftwareTerminology as TopicComparative StudyEvaluation StudyJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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Gabriel F Berriz, Oliver D King, Barbara Bryant, Chris Sander, Frederick P Roth. 2003-12-12. Characterizing gene sets with FuncAssociate.. https://doi.org/10.1093/bioinformatics%2Fbtg363

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