title: Activating and inhibiting connections in biological network dynamics.
abstract: 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.
  
  
  CONCLUSIONS
  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.
  
  
  METHODS
  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.
authors.affiliation: Department of Physics, University of Colorado, 390 UCB, Boulder, CO 80309, USA. daniel.mcdonald@colorado.edu
authors.forename: Daniel
authors.initials: D
authors.lastname: McDonald
authors.forename: Laura
authors.initials: L
authors.lastname: Waterbury
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.forename: M D
authors.initials: MD
authors.lastname: Betterton
mesh_terms: D000465:Algorithms; D000818:Animals; D017360:Arabidopsis / Q000235:genetics / Q000502:physiology; D002940:Circadian Rhythm / Q000235:genetics / Q000502:physiology; D004330:Drosophila / Q000235:genetics / Q000502:physiology; D053263:Gene Regulatory Networks; D055641:Mathematical Concepts; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D008957:Models, Genetic; D020932:Nerve Growth Factor / Q000235:genetics / Q000502:physiology; D051880:Receptors, Notch / Q000235:genetics / Q000502:physiology; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology; D049490:Systems Biology; D051153:Wnt Proteins / Q000235:genetics / Q000502:physiology; D051176:beta Catenin / Q000235:genetics / Q000502:physiology
chemical_list: D051880:Receptors, Notch; D051153:Wnt Proteins; D051176:beta Catenin; D020932:Nerve Growth Factor