Using Transcription Factor Binding Site Co-Occurrence to Predict Regulatory Regions

Holger Klein (
Martin Vingron (

Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, D-14195 Berlin, Germany


Transcription factors (TFs) bind to the regulatory regions of genes in a cooperative manner. This article describes a method to detect pairs of transcription factor binding sites which co-occur in known regulatory regions more often than expected by mere combination of the individual binding sites. We determine frequently co-occurring TF pairs and evaluate the method using known TF interactions. Furthermore we use co-occurrence scores to assess the regulatory potential of a sequence region by calculating a graph-based score. We show results for the score on known regulatory regions.

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Japanese Society for Bioinformatics