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J Theor Biol. 2013 Oct 21;335:130-46. doi: 10.1016/j.jtbi.2013.06.009. Epub 2013 Jun 15.

Dynamics and control at feedback vertex sets. II: a faithful monitor to determine the diversity of molecular activities in regulatory networks.

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Theoretical Biology Laboratory, RIKEN, Wako 351-0198, Japan.


Modern biology provides many networks describing regulations between many species of molecules. It is widely believed that the dynamics of molecular activities based on such regulatory networks are the origin of biological functions. However, we currently have a limited understanding of the relationship between the structure of a regulatory network and its dynamics. In this study we develop a new theory to provide an important aspect of dynamics from information of regulatory linkages alone. We show that the "feedback vertex set" (FVS) of a regulatory network is a set of "determining nodes" of the dynamics. The theory is powerful to study real biological systems in practice. It assures that (i) any long-term dynamical behavior of the whole system, such as steady states, periodic oscillations or quasi-periodic oscillations, can be identified by measurements of a subset of molecules in the network, and that (ii) the subset is determined from the regulatory linkage alone. For example, dynamical attractors possibly generated by a signal transduction network with 113 molecules can be identified by measurement of the activity of only 5 molecules, if the information on the network structure is correct. Our theory therefore provides a rational criterion to select key molecules to control a system. We also demonstrate that controlling the dynamics of the FVS is sufficient to switch the dynamics of the whole system from one attractor to others, distinct from the original.


Complex systems; Determining nodes; Feedback vertex set; Informative nodes; Regulatory networks

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