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GOToolBox: functional analysis of gene datasets based on Gene Ontology

David Martin1*, Christine Brun1, Elisabeth Remy2, Pierre Mouren1, Denis Thieffry1 and Bernard Jacq1

Author Affiliations

1 Laboratoire de Génétique et Physiologie du Développement, IBDM, CNRS/INSERM/Université de la Méditerranée, Parc Scientifique de Luminy, case 907, 13288 Marseille, France

2 Institut de Mathématiques de Luminy, Parc Scientifique de Luminy, 13288 Marseille, France

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Genome Biology 2004, 5:R101  doi:10.1186/gb-2004-5-12-r101

Published: 26 November 2004

Abstract

We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license.