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Models of transcription factor binding: Sensitivity of activation functions to model assumptions

Chu, Dominique, Zabet, Nicolae Radu, Mitavskiy, Boris (2009) Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology, 257 (3). pp. 419-429. ISSN 0022-5193. (doi:10.1016/j.jtbi.2008.11.026) (KAR id:24077)

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We present three models of how transcription factors (TFs) bind to their specific binding sites on the DNA: a model based on statistical physics, a Markov-chain model and a computational simulation. Comparison of these models suggests that the effect of non-specific binding can be significant. We also investigate possible mechanisms for cooperativity. The simulation model suggests that direct interactions between TFs are unlikely to be the main source of cooperativity between specific binding sites, because such interactions tend to lead to the formation of clusters on the DNA with undesirable side-effects.

Item Type: Article
DOI/Identification number: 10.1016/j.jtbi.2008.11.026
Uncontrolled keywords: Markov chain; Computational simulation; Partition function; Transcription factors; Cooperativity
Subjects: Q Science > QA Mathematics (inc Computing science) > QA 76 Software, computer programming,
Divisions: Divisions > Division of Computing, Engineering and Mathematical Sciences > School of Computing
Depositing User: Dominique Chu
Date Deposited: 29 Mar 2010 12:13 UTC
Last Modified: 16 Nov 2021 10:02 UTC
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Chu, Dominique:
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