Using transcription factor binding site co-occurrence to predict regulatory regions.
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.
Klein
Holger
H
Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, D-14195 Berlin, Germany. holger.klein@molgen.mpg.de
Vingron
Martin
M
D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012045:Regulatory Sequences, Nucleic Acid; D014157:Transcription Factors / Q000378:metabolism*
D014157:Transcription Factors; D004247:DNA