Explicit equilibrium modeling of transcription-factor binding and gene regulation

被引：93

作者：

Granek, JA

Clarke, ND

机构：

[1] Johns Hopkins Univ, Sch Med, Dept Biophys & Biophys Chem, Baltimore, MD 21205 USA

[2] Natl Evolutionary Synth Ctr, Durham, NC 27705 USA

[3] Genome Inst Singapore, Singapore 138672, Singapore

来源：

GENOME BIOLOGY | 2005年 / 6卷 / 10期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1186/gb-2005-6-10-r87

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

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页数：10

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