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Bull Math Biol. 2011 Apr;73(4):873-98. doi: 10.1007/s11538-010-9609-1. Epub 2010 Dec 18.

Analysis of discrete bioregulatory networks using symbolic steady states.

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1
DFG Research Center Matheon, Freie Universit├Ąt Berlin, Germany. siebert@mi.fu-berlin.de

Abstract

A discrete model of a biological regulatory network can be represented by a discrete function that contains all available information on interactions between network components and the rules governing the evolution of the network in a finite state space. Since the state space size grows exponentially with the number of network components, analysis of large networks is a complex problem. In this paper, we introduce the notion of symbolic steady state that allows us to identify subnetworks that govern the dynamics of the original network in some region of state space. We state rules to explicitly construct attractors of the system from subnetwork attractors. Using the results, we formulate sufficient conditions for the existence of multiple attractors resp. a cyclic attractor based on the existence of positive resp. negative feedback circuits in the graph representing the structure of the system. In addition, we discuss approaches to finding symbolic steady states. We focus both on dynamics derived via synchronous as well as asynchronous update rules. Lastly, we illustrate the results by analyzing a model of T helper cell differentiation.

PMID:
21170598
DOI:
10.1007/s11538-010-9609-1
[Indexed for MEDLINE]
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