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A classification based framework for quantitative description of large-scale microarray data

Dipen P Sangurdekar12, Friedrich Srienc12 and Arkady B Khodursky23*

Author Affiliations

1 Department of Chemical Engineering and Materials Science, University of Minnesota, Saint Paul, MN 55108, USA

2 Biotechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA

3 Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, MN 55108, USA

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Genome Biology 2006, 7:R32  doi:10.1186/gb-2006-7-4-r32

Published: 20 April 2006

Abstract

Genome-wide surveys of transcription depend on gene classifications for the purpose of data interpretation. We propose a new information-theoretical-based method to: assess significance of co-expression within any gene group; quantitatively describe condition-specific gene-class activity; and systematically evaluate conditions in terms of gene-class activity. We applied this technique to describe microarray data tracking Escherichia coli transcriptional responses to more than 30 chemical and physiological perturbations. We correlated the nature and breadth of the responses with the nature of perturbation, identified gene group proxies for the perturbation classes and quantitatively compared closely related physiological conditions.