Memory functions reveal structural properties of gene regulatory networks.

PLoS Computational Biology
Edgar Herrera-DelgadoPeter Sollich

Abstract

Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and complexity of these models mean that their behaviour is not always intuitive and the underlying mechanisms can be difficult to decipher. For this reason, methods that simplify and aid exploration of complex networks are necessary. To this end we develop a broadly applicable form of the Zwanzig-Mori projection. By first converting a thermodynamic state ensemble model of gene regulation into mass action reactions we derive a general method that produces a set of time evolution equations for a subset of components of a network. The influence of the rest of the network, the bulk, is captured by memory functions that describe how the subnetwork reacts to its own past state via components in the bulk. These memory functions provide probes of near-steady state dynamics, revealing information not easily accessible otherwise. We illustrate the method on a simple cross-repressive transcriptional motif to show that memory functions not only simplify the analysis of the subnetwork but also have a natural interpre...Continue Reading

References

Jan 20, 1985·Journal of Molecular Biology·M A Shea, G K Ackers
Apr 1, 1973·Journal of Theoretical Biology·L Glass, S A Kauffman
Mar 29, 2000·Proceedings of the National Academy of Sciences of the United States of America·A J ChorinR Kupferman
Feb 19, 2002·Chemical Reviews·Miles S. Okino, Michael L. Mavrovouniotis
Mar 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Michael Levine, Eric H Davidson
Mar 31, 2005·Current Opinion in Genetics & Development·Lacramioara BintuRob Phillips
May 20, 2006·PLoS Computational Biology·Theodore J PerkinsLeon Glass
Jun 1, 2006·Proceedings of the National Academy of Sciences of the United States of America·Gheorghe CraciunMartin Feinberg
Sep 5, 2006·Developmental Cell·Alex MogilnerWallace F Marshall
May 19, 2007·Nature Reviews. Genetics·Uri Alon
Oct 31, 2008·Nature Reviews. Molecular Cell Biology·Béla Novák, John J Tyson
Feb 18, 2010·Developmental Cell·David M UmulisHans G Othmer
Aug 31, 2010·Trends in Cell Biology·Hernan G GarciaRob Phillips
Sep 9, 2011·BMC Systems Biology·Mikael SunnåkerMats Jirstrand
Apr 3, 2012·Journal of Theoretical Biology·Mochamad ApriJaap Molenaar
Apr 6, 2012·PLoS Computational Biology·Marc S Sherman, Barak A Cohen
Jun 4, 2013·Current Opinion in Genetics & Development·Michael CohenRobert Blassberg
Jul 26, 2013·Journal of the Royal Society, Interface·Elisenda Feliu, Carsten Wiuf
Jun 15, 2014·Journal of Theoretical Biology·Katy J RubinTony Ng
Aug 17, 2014·BMC Systems Biology·Luca Cardelli
May 10, 2016·The Journal of Chemical Physics·Katy J Rubin, Peter Sollich
Jun 15, 2016·Physical Review. E·Stephen Smith, Ramon Grima

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