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Bioinformatics Advance Access published online on September 17, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn492
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

FunNet: an integrative tool for exploring transcriptional interactions

Edi Prifti 1,2,4,*, Jean-Daniel Zucker 1,4, Karine Clement 1,2,3 and Corneliu Henegar 1,*

1INSERM, UMR-S 872, Les Cordeliers, Eq. 7 Nutriomique, Paris, F-75006 France; 2Pierre et Marie Curie-Paris 6 Univer-sity, Cordeliers Research Center, UMR-S 872, Paris, F-75006 France; 3Assistance Publique-Hôpitaux de Paris, Pitié Salpôtrière Hospital, Nutrition and Endocrinology department, Paris, F-75013 France; 4IRD UR Géodes, Centre IRD de l'Ile de France, Bondy, F-93143 France.

*To whom correspondence should be addressed. Dr. Corneliu Henegar, E-mail: corneliu{at}henegar.info, chnr{at}free.fr


  Abstract

Summary: We describe here an exploratory tool, called FunNet, which implements an original systems biology approach, aiming to improve the biological relevance of the modular interaction patterns identified in transcriptional co-expression networks. A suitable analytical model, involving two abstraction layers, has been devised to relate expression profiles to the knowledge on transcripts' biological roles, extracted from genomic databases, into a comprehensive exploratory framework. This approach has been implemented into a user-friendly web tool to promote its open use by the community.

Availability: http://www.funnet.info

Contact: edi.prifti{at}crc.jussieu.fr

Associate Editor: Prof. John Quackenbush

Received on June 17, 2008; revised on July 23, 2008; accepted on September 12, 2008

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