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Unraveling the Design Principle for Motif Organization in Signaling Networks

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  • Samrat Chatterjee
  • Dhiraj Kumar

Abstract

Cellular signaling networks display complex architecture. Defining the design principle of this architecture is crucial for our understanding of various biological processes. Using a mathematical model for three-node feed-forward loops, we identify that the organization of motifs in specific manner within the network serves as an important regulator of signal processing. Further, incorporating a systemic stochastic perturbation to the model we could propose a possible design principle, for higher-order organization of motifs into larger networks in order to achieve specific biological output. The design principle was then verified in a large, complex human cancer signaling network. Further analysis permitted us to classify signaling nodes of the network into robust and vulnerable nodes as a result of higher order motif organization. We show that distribution of these nodes within the network at strategic locations then provides for the range of features displayed by the signaling network.

Suggested Citation

  • Samrat Chatterjee & Dhiraj Kumar, 2011. "Unraveling the Design Principle for Motif Organization in Signaling Networks," PLOS ONE, Public Library of Science, vol. 6(12), pages 1-9, December.
    • Handle: RePEc:plo:pone00:0028606
    DOI: 10.1371/journal.pone.0028606
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    References listed on IDEAS

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    1. Liang Qiao & Robert B Nachbar & Ioannis G Kevrekidis & Stanislav Y Shvartsman, 2007. "Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling," PLOS Computational Biology, Public Library of Science, vol. 3(9), pages 1-8, September.
    2. Julian Downward, 2001. "The ins and outs of signalling," Nature, Nature, vol. 411(6839), pages 759-762, June.
    3. Leland H. Hartwell & John J. Hopfield & Stanislas Leibler & Andrew W. Murray, 1999. "From molecular to modular cell biology," Nature, Nature, vol. 402(6761), pages 47-52, December.
    4. Steven H. Strogatz, 2001. "Exploring complex networks," Nature, Nature, vol. 410(6825), pages 268-276, March.
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