CLARE: Cracking the LAnguage of Regulatory Elements

• DOI: 10.1093/bioinformatics/btr704
• Publication Date: 2011-12-24T02:37:52Z
• Authors: Leila Taher; Leelavati Narlikar; Ivan Ovcharenko
• Keywords: 0301 basic medicine; 0206 medical engineering; Genomics; 02 engineering and technology; Regulatory Sequences, Nucleic Acid; Mice; 03 medical and health sciences; Enhancer Elements, Genetic; Prosencephalon; Gene Expression Regulation; Organ Specificity; Animals; Humans; Software; Transcription Factors

AbstractSummary: CLARE is a computational method designed to reveal sequence encryption of tissue-specific regulatory elements. Starting with a set of regulatory elements known to be active in a particular tissue/process, it learns the sequence code of the input set and builds a predictive model from features specific to those elements. The resulting model can then be applied to user-supplied genomic regions to identify novel candidate regulatory elements. CLARE's model also provides a detailed analysis of transcription factors that most likely bind to the elements, making it an invaluable tool for understanding mechanisms of tissue-specific gene regulation.Availability: CLARE is freely accessible at http://clare.dcode.org/.Contact: [e-mail]; [e-mail] information: Supplementary data are available at Bioinformatics online.