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Dynamic Properties of Network Motifs Contribute to Biological Network Organization

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  • Robert J Prill
  • Pablo A Iglesias
  • Andre Levchenko

Abstract

Biological networks, such as those describing gene regulation, signal transduction, and neural synapses, are representations of large-scale dynamic systems. Discovery of organizing principles of biological networks can be enhanced by embracing the notion that there is a deep interplay between network structure and system dynamics. Recently, many structural characteristics of these non-random networks have been identified, but dynamical implications of the features have not been explored comprehensively. We demonstrate by exhaustive computational analysis that a dynamical property—stability or robustness to small perturbations—is highly correlated with the relative abundance of small subnetworks (network motifs) in several previously determined biological networks. We propose that robust dynamical stability is an influential property that can determine the non-random structure of biological networks. The authors model how network motifs respond to small-scale perturbations and find a strong correlation between motif stability and abundance in a network, suggesting that dynamic properties of network motifs may play a role in overall network structure.

Suggested Citation

  • Robert J Prill & Pablo A Iglesias & Andre Levchenko, 2005. "Dynamic Properties of Network Motifs Contribute to Biological Network Organization," PLOS Biology, Public Library of Science, vol. 3(11), pages 1-1, October.
  • Handle: RePEc:plo:pbio00:0030343
    DOI: 10.1371/journal.pbio.0030343
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    1. Christopher T. Harbison & D. Benjamin Gordon & Tong Ihn Lee & Nicola J. Rinaldi & Kenzie D. Macisaac & Timothy W. Danford & Nancy M. Hannett & Jean-Bosco Tagne & David B. Reynolds & Jane Yoo & Ezra G., 2004. "Transcriptional regulatory code of a eukaryotic genome," Nature, Nature, vol. 431(7004), pages 99-104, September.
    2. U. Alon & M. G. Surette & N. Barkai & S. Leibler, 1999. "Robustness in bacterial chemotaxis," Nature, Nature, vol. 397(6715), pages 168-171, January.
    3. Olaf Sporns & Rolf Kötter, 2004. "Motifs in Brain Networks," PLOS Biology, Public Library of Science, vol. 2(11), pages 1-1, October.
    4. Sen Song & Per Jesper Sjöström & Markus Reigl & Sacha Nelson & Dmitri B Chklovskii, 2005. "Highly Nonrandom Features of Synaptic Connectivity in Local Cortical Circuits," PLOS Biology, Public Library of Science, vol. 3(3), pages 1-1, March.
    5. N. Barkai & S. Leibler, 1997. "Robustness in simple biochemical networks," Nature, Nature, vol. 387(6636), pages 913-917, June.
    6. Nicholas M. Luscombe & M. Madan Babu & Haiyuan Yu & Michael Snyder & Sarah A. Teichmann & Mark Gerstein, 2004. "Genomic analysis of regulatory network dynamics reveals large topological changes," Nature, Nature, vol. 431(7006), pages 308-312, September.
    7. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
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