tailieunhanh - Báo cáo y học: "A distance difference matrix approach to identifying transcription factors that regulate differential gene expression"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Critical Care giúp cho các bạn có thêm kiến thức về ngành y học đề tài: A distance difference matrix approach to identifying transcription factors that regulate differential gene expression. | Method Open Access A distance difference matrix approach to identifying transcription factors that regulate differential gene expression Pieter De Bleser n Bart Hooghe n Dominique Vlieghe and Frans van Royn Addresses Bioinformatics Core VIB B-9052 Ghent Belgium. Department for Molecular Biomedical Research VIB B-9052 Ghent Belgium. Department of Molecular Biology Ghent University B-9052 Ghent Belgium. Correspondence Pieter De Bleser. Email pieterdb@ Published 16 May 2007 Genome Biology 2007 8 R83 doi 186 gb-2007-8-5-r83 The electronic version of this article is the complete one and can be found online at http 2007 8 5 R83 Received 16 November 2006 Revised 30 March 2007 Accepted 16 May 2007 2007 De Bleser et al. licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract We introduce a method that considers target genes of a transcription factor and searches for transcription factor binding sites TFBSs of secondary factors responsible for differential responses among these targets. Based on the distance difference matrix concept the method simultaneously integrates statistical overrepresentation and co-occurrence of TFBSs. Our approach is validated on datasets of differentially regulated human genes and is shown to be highly effective in detecting TFBSs responsible for the observed differential gene expression. Background Eukaryotic genes are transcriptionally regulated by the coordinated interaction of multiple transcription factors with arrays of transcription factor binding sites TFBSs and with each other. Arrays of TFBSs referred to as cz s-regulatory modules CRMs 1 2 are usually situated upstream of the genes they regulate. A simple strategy based on the assumption that co-expression .