A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
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
Genome Biology 2007, 8:R83 doi:10.1186/gb-2007-8-5-r83Published: 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.