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BMCBI
2006

Predicting transcription factor binding sites using local over-representation and comparative genomics

11 years 1 months ago
Predicting transcription factor binding sites using local over-representation and comparative genomics
Background: Identifying cis-regulatory elements is crucial to understanding gene expression, which highlights the importance of the computational detection of overrepresented transcription factor binding sites (TFBSs) in coexpressed or coregulated genes. However, this is a challenging problem, especially when considering higher eukaryotic organisms. Results: We have developed a method, named TFM-Explorer, that searches for locally overrepresented TFBSs in a set of coregulated genes, which are modeled by profiles provided by a database of position weight matrices. The novelty of the method is that it takes advantage of spatial conservation in the sequence and supports multiple species. The efficiency of the underlying algorithm and its robustness to noise allow weak regulatory signals to be detected in large heterogeneous data sets. Conclusion: TFM-Explorer provides an efficient way to predict TFBS overrepresentation in related sequences. Promising results were obtained in a variety of...
Matthieu Defrance, Hélène Touzet
Added 10 Dec 2010
Updated 10 Dec 2010
Type Journal
Year 2006
Where BMCBI
Authors Matthieu Defrance, Hélène Touzet
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