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Bioinformatics Advance Access published online on January 18, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn015
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

HCGene: a software tool to support the hierarchical classification of genes

Giorgio Valentini * and Nicolò Cesa-Bianchi

DSI; Dip. di Scienze dell'Informazione, Università degli Studi di Milano, Via Comelico 39, Italy.

*To whom correspondence should be addressed. Dr. Giorgio Valentini, E-mail: valentini{at}dsi.unimi.it


  Abstract

Motivation: The R package HCGene (Hierarchical Classification of Genes) implements methods to process and analyze the Gene Ontology and the FunCat taxonomy in order to support the functional classification of genes. HCGene allows the extraction of subgraphs and subtrees related to specific biological problems, the labelling of genes and gene products with multiple and hierarchical functional classes, and the association of different types of bio-molecular data to genes for learning to predict their functions.

Availability: http://homes.dsi.unimi.it/~valenti/SW/hcgene/download/hcgene_1.0.tar.gz

Contact: valentini{at}dsi.unimi.it

Supplementary Information: http://homes.dsi.unimi.it/~valenti/SW/hcgene

Associate Editor: Prof. Martin Bishop

Received on November 9, 2007; revised on December 20, 2007; accepted on January 8, 2008

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