Explicit equilibrium modeling of transcription-factor binding and gene regulation.docVIP

Open Access Me od 2005GranekVolumtheand6, IsClarkesue 10, Article R87 Explicit equilibrium modeling of transcription-factor binding and gene regulation Joshua A Granek*? and Neil D Clarke*? Addresses: *Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, North Wolfe Street, Baltimore, MD 21205, USA. ?National Evolutionary Synthesis Center, Broad Street, Durham, NC 27705, USA. ?Genome Institute of Singapore, Biopolis Street, Singapore 138672, Republic of Singapore. Correspondence: Neil D Clarke. E-mail: nclarke@ Published: 30 September 2005 Received: 3 May 2005 Revised: 17 June 2005 Accepted: 30 August 2005 Genome Biology 2005, 6:R87 (doi:10.1186/gb-2005-6-10-r87) The electronic version of this article is the complete one and can be found online at /2005/6/10/R87 ? 2005 Granek and Clarke; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ExplicitcopmApectoitequilibriummiopnu.ta/tpionalmodelingmodel, GOofMtranscription-factorER, is presented thabindingt predicandts tragenenscriregulationption-factor binding and incorporates effects of cooperativity and Abstract We have developed a computational model that predicts the probability of transcription factor binding to any site in the genome. GOMER (generalizable occupancy model of expression regulation) calculates binding probabilities on the basis of position weight matrices, and incorporates the effects of cooperativity and competition by explicit calculation of coupled binding equilibria. GOMER can be used to test hypotheses regarding gene regulation that build upon this physically principled prediction of protein-DNA binding. Background implicit model is that gene regulation is mediated by