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Activating and inhibiting connections in biological network dynamics

BACKGROUND: Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dyna...

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Detalles Bibliográficos
Autores principales: McDonald, Daniel, Waterbury, Laura, Knight, Rob, Betterton, M D
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651858/
https://www.ncbi.nlm.nih.gov/pubmed/19055800
http://dx.doi.org/10.1186/1745-6150-3-49
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author McDonald, Daniel
Waterbury, Laura
Knight, Rob
Betterton, M D
author_facet McDonald, Daniel
Waterbury, Laura
Knight, Rob
Betterton, M D
author_sort McDonald, Daniel
collection PubMed
description BACKGROUND: Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior – for example, whether deleting a protein from a signaling network would maintain the network's dynamical behavior, or induce oscillations or chaos. RESULTS: Here we report that the balance between activating and inhibiting connections is important in determining whether network dynamics reach steady state or oscillate. We use a simple dynamical model of a network of interacting genes or proteins. Using the model, we study random networks, networks selected for robust dynamics, and examples of biological network topologies. The fraction of activating connections influences whether the network dynamics reach steady state or oscillate. CONCLUSION: The activating fraction may predispose a network to oscillate or reach steady state, and neutral evolution or selection of this parameter may affect the behavior of biological networks. This principle may unify the dynamics of a wide range of cellular networks. REVIEWERS: Reviewed by Sergei Maslov, Eugene Koonin, and Yu (Brandon) Xia (nominated by Mark Gerstein). For the full reviews, please go to the Reviewers' comments section.
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spelling pubmed-26518582009-03-09 Activating and inhibiting connections in biological network dynamics McDonald, Daniel Waterbury, Laura Knight, Rob Betterton, M D Biol Direct Research BACKGROUND: Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior – for example, whether deleting a protein from a signaling network would maintain the network's dynamical behavior, or induce oscillations or chaos. RESULTS: Here we report that the balance between activating and inhibiting connections is important in determining whether network dynamics reach steady state or oscillate. We use a simple dynamical model of a network of interacting genes or proteins. Using the model, we study random networks, networks selected for robust dynamics, and examples of biological network topologies. The fraction of activating connections influences whether the network dynamics reach steady state or oscillate. CONCLUSION: The activating fraction may predispose a network to oscillate or reach steady state, and neutral evolution or selection of this parameter may affect the behavior of biological networks. This principle may unify the dynamics of a wide range of cellular networks. REVIEWERS: Reviewed by Sergei Maslov, Eugene Koonin, and Yu (Brandon) Xia (nominated by Mark Gerstein). For the full reviews, please go to the Reviewers' comments section. BioMed Central 2008-12-04 /pmc/articles/PMC2651858/ /pubmed/19055800 http://dx.doi.org/10.1186/1745-6150-3-49 Text en Copyright © 2008 McDonald et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
McDonald, Daniel
Waterbury, Laura
Knight, Rob
Betterton, M D
Activating and inhibiting connections in biological network dynamics
title Activating and inhibiting connections in biological network dynamics
title_full Activating and inhibiting connections in biological network dynamics
title_fullStr Activating and inhibiting connections in biological network dynamics
title_full_unstemmed Activating and inhibiting connections in biological network dynamics
title_short Activating and inhibiting connections in biological network dynamics
title_sort activating and inhibiting connections in biological network dynamics
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651858/
https://www.ncbi.nlm.nih.gov/pubmed/19055800
http://dx.doi.org/10.1186/1745-6150-3-49
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