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Open Access Method

Explicit equilibrium modeling of transcription-factor binding and gene regulation

Joshua A Granek12 and Neil D Clarke13*

Author Affiliations

1 Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, North Wolfe Street, Baltimore, MD 21205, USA

2 National Evolutionary Synthesis Center, Broad Street, Durham, NC 27705, USA

3 Genome Institute of Singapore, Biopolis Street, Singapore 138672, Republic of Singapore

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Genome Biology 2005, 6:R87  doi:10.1186/gb-2005-6-10-r87

Published: 30 September 2005

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.