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A distance difference matrix approach to identifying transcription factors that regulate differential gene expression

Pieter De Bleser123*, Bart Hooghe123, Dominique Vlieghe123 and Frans van Roy23

Author Affiliations

1 Bioinformatics Core, VIB, B-9052 Ghent, Belgium

2 Department for Molecular Biomedical Research, VIB, B-9052 Ghent, Belgium

3 Department of Molecular Biology, Ghent University, B-9052 Ghent, Belgium

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Genome Biology 2007, 8:R83  doi:10.1186/gb-2007-8-5-r83

Published: 16 May 2007


We introduce a method that considers target genes of a transcription factor, and searches for transcription factor binding sites (TFBSs) of secondary factors responsible for differential responses among these targets. Based on the distance difference matrix concept, the method simultaneously integrates statistical overrepresentation and co-occurrence of TFBSs. Our approach is validated on datasets of differentially regulated human genes and is shown to be highly effective in detecting TFBSs responsible for the observed differential gene expression.