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Bioinformatics Advance Access published online on May 12, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm252
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BioMoby Web services to support clustering of co-regulated genes based on similarity of promoter configurations

Arnaud Kerhornou *,1,2,3 and Roderic Guigó 1,2

1 Centre de Regulacio Genomica, Pg. Maritim de la Barceloneta, 08003 Barcelona, Catalonia, Spain.
2 Research Group in Biomedical Informatics, Institut Municipal d'Investigació Mèdica and Universitat Pompeu Fabra, Pg. Maritim de la Barceloneta, 08003 Barcelona, Catalonia, Spain.
3 EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

*To whom correspondence should be addressed. Mr. Arnaud Kerhornou, E-mail: arnaud.kerhornou{at}crg.es, roderic.guigo{at}crg.es


  Abstract

Summary Here we present a computational protocol to analyse the promoter regions of a given set of co-expressed genes, and its implementation through the use of Web services technologies. This protocol aims to cluster a set of co-regulated genes in subsets of genes showing similar configurations of Transcription Factor Binding Sites. All the steps of this protocol have been developed as Web services that are compliant with BioMoby specifications.

Availability: {{http://genome.imim.es/cgi-bin/moby/GeneClustering_DataSubmission.cgi}}

Associate Editor: Prof. Alfonso Valencia

Received on December 22, 2006; revised on April 23, 2007; accepted on May 4, 2007

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