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Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space

Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have foun...

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Autores principales: Ahnert, S. E., Fink, T. M. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971217/
https://www.ncbi.nlm.nih.gov/pubmed/27440255
http://dx.doi.org/10.1098/rsif.2016.0179
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author Ahnert, S. E.
Fink, T. M. A.
author_facet Ahnert, S. E.
Fink, T. M. A.
author_sort Ahnert, S. E.
collection PubMed
description Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the ‘function’ of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature.
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spelling pubmed-49712172016-08-04 Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space Ahnert, S. E. Fink, T. M. A. J R Soc Interface Life Sciences–Physics interface Network motifs have been studied extensively over the past decade, and certain motifs, such as the feed-forward loop, play an important role in regulatory networks. Recent studies have used Boolean network motifs to explore the link between form and function in gene regulatory networks and have found that the structure of a motif does not strongly determine its function, if this is defined in terms of the gene expression patterns the motif can produce. Here, we offer a different, higher-level definition of the ‘function’ of a motif, in terms of two fundamental properties of its dynamical state space as a Boolean network. One is the basin entropy, which is a complexity measure of the dynamics of Boolean networks. The other is the diversity of cyclic attractor lengths that a given motif can produce. Using these two measures, we examine all 104 topologically distinct three-node motifs and show that the structural properties of a motif, such as the presence of feedback loops and feed-forward loops, predict fundamental characteristics of its dynamical state space, which in turn determine aspects of its functional versatility. We also show that these higher-level properties have a direct bearing on real regulatory networks, as both basin entropy and cycle length diversity show a close correspondence with the prevalence, in neural and genetic regulatory networks, of the 13 connected motifs without self-interactions that have been studied extensively in the literature. The Royal Society 2016-07 /pmc/articles/PMC4971217/ /pubmed/27440255 http://dx.doi.org/10.1098/rsif.2016.0179 Text en © 2016 The Authors. http://creativecommons.org/licenses/by/4.0/ Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
spellingShingle Life Sciences–Physics interface
Ahnert, S. E.
Fink, T. M. A.
Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space
title Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space
title_full Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space
title_fullStr Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space
title_full_unstemmed Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space
title_short Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space
title_sort form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space
topic Life Sciences–Physics interface
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971217/
https://www.ncbi.nlm.nih.gov/pubmed/27440255
http://dx.doi.org/10.1098/rsif.2016.0179
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