CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated

Background: The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current approaches. Computational methods to reduce false positives are to look for overrepresentation of transcription factor binding sites in a set of similarly regulated promoters or to look for conservation in orthologous promoter alignments. Results: We have developed a novel tool, "CORE_TF" (Conserved and Over-REpresented Transcription Factor binding sites) that identifies common transcription factor binding sites in promoters of co-regulated genes. To improve upon existing binding site predictions, the tool searches for position weight matrices from the TRANSFACR database that are over-represented in an experimental set compared to a random set of promoters and identifies cross-species conservation of the predicted transcription factor binding sites. The algorit...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Matthew S. Hestand, Michiel van Galen, Michel P. Villerius, Gert-Jan B. van Ommen, Johan T. den Dunnen, Peter A. C. 't Hoen
• Keywords: BMCBI 2008, False Positives, Promoters, Transcription Factors