Explicit equilibrium modeling of transcription-factor binding and gene regulation
Joshua A Granek, Neil D Clarke
TL;DR
A new model called GOMER predicts how transcription factors bind to DNA, considering interactions between them.
Contribution
GOMER introduces a physically principled approach to model transcription factor binding with cooperativity and competition.
Findings
GOMER calculates binding probabilities using position weight matrices.
The model incorporates effects of cooperativity and competition through equilibrium calculations.
Abstract
A computational model, GOMER, is presented that predicts transcription-factor binding and incorporates effects of cooperativity and competition. 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.
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
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Taxonomy
TopicsAgriculture and Rural Development Research · Migration, Identity, and Health · Aging, Elder Care, and Social Issues