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Genome Biol. 2005;6(10):R87. Epub 2005 Sep 30.

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

Author information

  • 1Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. jgranek@jhmi.edu

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.

PMID:
16207358
[PubMed - indexed for MEDLINE]
PMCID:
PMC1257470
Free PMC Article

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