Chu, Dominique and Zabet, Nicolae Radu and Mitavskiy, Boris (2009) Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology, 257 (3). pp. 419-429. DOI https://doi.org/10.1016/j.jtbi.2008.11.026
Chu, Dominique and Zabet, Nicolae Radu and Mitavskiy, Boris (2009) Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology, 257 (3). pp. 419-429. DOI https://doi.org/10.1016/j.jtbi.2008.11.026
Chu, Dominique and Zabet, Nicolae Radu and Mitavskiy, Boris (2009) Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology, 257 (3). pp. 419-429. DOI https://doi.org/10.1016/j.jtbi.2008.11.026
Abstract
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. © 2008 Elsevier Ltd. All rights reserved.
Item Type: | Article |
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Uncontrolled Keywords: | Markov chain; Computational simulation; Partition function; Transcription factors; Cooperativity |
Subjects: | Q Science > QC Physics Q Science > QH Natural history > QH426 Genetics |
Divisions: | Faculty of Science and Health Faculty of Science and Health > Life Sciences, School of |
SWORD Depositor: | Unnamed user with email elements@essex.ac.uk |
Depositing User: | Unnamed user with email elements@essex.ac.uk |
Date Deposited: | 04 Feb 2016 19:43 |
Last Modified: | 30 Oct 2024 16:10 |
URI: | http://repository.essex.ac.uk/id/eprint/15108 |