TFBScluster: a resource for the characterization of transcriptional regulatory networks

• Published in: Bioinformatics 2005-07, Vol.21 (13), p.3058-3059
• Main Authors: Donaldson, Ian John, Chapman, Michael, Göttgens, Berthold
• Format: Article
• Language: English
• Subjects: Algorithms; Base Sequence; Binding Sites; Chromosome Mapping - methods; Cluster Analysis; Conserved Sequence; Gene Expression Regulation - genetics; Molecular Sequence Data; Promoter Regions, Genetic - genetics; Protein Binding; Sequence Alignment - methods; Sequence Analysis, DNA - methods; Sequence Homology, Nucleic Acid; Software; Transcription Factors - genetics; Transcription, Genetic - genetics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti461

One major challenge of the post-sequencing era of the human genome project will be the functional annotation of the non-coding portion of the genome, in particular gene regulatory sequences. We have developed a new web-based tool, TFBScluster, which performs genome-wide identification of transcription factor binding site clusters that are conserved in multiple mammalian genomes. Clusters representing candidate gene regulatory elements can be filtered further, based on the presence or absence of additional user-defined DNA sequence motifs or by constraining the orientation or order of binding sites. Comprehensive results files, returned by email, are designed to facilitate experimental validation of computationally identified candidate gene regulatory sequences. TFBScluster, therefore, has the potential to contribute to deciphering transcriptional networks that regulate a wide range of mammalian developmental processes. Availability: http://hscl.cimr.cam.ac.uk/TFBScluster_genome_34.html Contact: [e-mail] Supplementary information: http://hscl.cimr.cam.ac.uk/sup_don05_app_api.html