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Bioinformatics Advance Access originally published online on September 7, 2007
Bioinformatics 2007 23(17):2306-2313; doi:10.1093/bioinformatics/btm335
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A novel non-overlapping bi-clustering algorithm for network generation using living cell array data

E. Yang 1, P.T. Foteinou 1, K.R. King 2, M.L. Yarmush 1,2 and I.P. Androulakis 1,*

1Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854 and 2Center for Engineering in Medicine/Surgical Services, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The living cell array quantifies the contribution of activated transcription factors upon the expression levels of their target genes. The direct manipulation of the regulatory mechanisms offers enormous possibilities for deciphering the machinery that activates and controls gene expression. We propose a novel bi-clustering algorithm for generating non-overlapping clusters of reporter genes and conditions and demonstrate how this information can be interpreted in order to assist in the construction of transcription factor interaction networks.

Contact: Yannis{at}rci.rutgers.edu

Associate Editor: Olga Troyanskaya

Received on May 6, 2007; revised on June 18, 2007; accepted on June 18, 2007

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