title: Most networks in Wagner's model are cycling.
abstract: In this paper we study a model of gene networks introduced by Andreas Wagner in the 1990s that has been used extensively to study the evolution of mutational robustness. We investigate a range of model features and parameters and evaluate the extent to which they influence the probability that a random gene network will produce a fixed point steady state expression pattern. There are many different types of models used in the literature, (discrete/continuous, sparse/dense, small/large network) and we attempt to put some order into this diversity, motivated by the fact that many properties are qualitatively the same in all the models. Our main result is that random networks in all models give rise to cyclic behavior more often than fixed points. And although periodic orbits seem to dominate network dynamics, they are usually considered unstable and not allowed to survive in previous evolutionary studies. Defining stability as the probability of fixed points, we show that the stability distribution of these networks is highly robust to changes in its parameters. We also find sparser networks to be more stable, which may help to explain why they seem to be favored by evolution. We have unified several disconnected previous studies of this class of models under the framework of stability, in a way that had not been systematically explored before.
authors.affiliation: Department of Biology, Stanford University, Stanford, California, United States of America. rpinho@stanford.edu
authors.forename: Ricardo
authors.initials: R
authors.lastname: Pinho
authors.forename: Elhanan
authors.initials: E
authors.lastname: Borenstein
authors.forename: Marcus W
authors.initials: MW
authors.lastname: Feldman
mesh_terms: D003198:Computer Simulation; D053263:Gene Regulatory Networks; D008957:Models, Genetic