tailieunhanh - Báo cáo y học: " Detecting DNA regulatory motifs by incorporating positional trends in information content"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Detecting DNA regulatory motifs by incorporating positional trends in information content. | Method Open Access Detecting DNA regulatory motifs by incorporating positional trends in information content Katherina J Kechris Erik van Zwet Peter J Bickel and Michael B Eisen Addresses Department of Statistics University of California Berkeley CA 94720 USA. Department of Genome Sciences Life Sciences Division Ernest Orlando Lawrence Berkeley National Lab Cyclotron Road Berkeley CA 94720 USA. Center for Integrative Genomics Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA. Current address Department of Biochemistry and Biophysics 600 16th Street 2240 University of California San Francisco CA 94143 USA. Current address Mathematical Institute University Leiden 2300 RA Leiden The Netherlands. Correspondence Katherina J Kechris. E-mail kechris@ Published 24 June 2004 Genome Biology 2004 5 R50 The electronic version of this article is the complete one and can be found online at http 2004 5 7 R50 Received 23 January 2004 Revised 4 May 2004 Accepted 4 May 2004 2004 Kechris et al. licensee BioMed Central Ltd. This is an Open Access article verbatim copying and redistribution of this article are permitted in all media for any purpose provided this notice is preserved along with the article s original URL. Abstract On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif. Background DNA-binding transcription factors have a crucial role in transcriptional regulation linking nuclear DNA to the transcriptional regulatory machinery in a sequence-specific manner. .