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Function constrains network architecture and dynamics: a case study on the yeast cell cycle Boolean network.

Kai-Yeung Lau1, Surya Ganguli, Chao Tang

  • 1Graduate Group in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA 94158-2517, USA.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|August 7, 2007
PubMed
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Biological network function constrains structure and dynamics. A new method, using a functional null model, reveals evolutionary pressures on the yeast cell cycle network, favoring ordered dynamics over robustness.

Area of Science:

  • Systems Biology
  • Computational Biology
  • Evolutionary Biology

Background:

  • Prior studies often link specific structures (e.g., scale-free) to function.
  • Understanding how function shapes network properties remains a challenge.
  • Biological networks exhibit complex structures and dynamics crucial for cellular processes.

Purpose of the Study:

  • To develop a general method for exploring functional constraints on biological network structure and dynamics.
  • To create a "functional null model" for assessing the significance of network features.
  • To identify evolutionary selection pressures on network properties.

Main Methods:

  • Developed a general method to analyze functional constraints on biological networks.
  • Constructed an algorithm to sample maximum entropy distributions of Boolean dynamical networks.

Related Experiment Videos

  • Applied the method to the yeast cell cycle gene expression cascade.

    • Main Results:

    • The functional null model revealed significant constraints on the yeast cell cycle network's architecture.
    • Identified strong selection pressures favoring ordered and convergent dynamics.
    • Observed a potential trade-off between dynamic properties and robustness to perturbations.

    Conclusions:

    • Network function significantly constrains both structure and dynamics.
    • Evolutionary pressures may prioritize specific dynamic behaviors in biological networks.
    • The yeast cell cycle network's properties suggest a selection for ordered dynamics, potentially impacting robustness.