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

Pieter De Bleser¹^,2^,3 , Bart Hooghe¹^,2^,3 , Dominique Vlieghe¹^,2^,3 and Frans van Roy²^,3

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

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

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

author email corresponding author email

Genome Biology 2007, 8:R83doi:10.1186/gb-2007-8-5-r83


Published:	16 May 2007

Subject areas: Bioinformatics, Genome studies

Abstract

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.