Combinatorics on update digraphs in Boolean networks Original Research Article

Boolean networks have been used as models of gene regulation and other biological networks. One key element in these models is the update schedule, which indicates the order in which states have to be updated. In Aracena et al. (2009) , the authors define equivalence classes that relate deterministic update schedules that yield the same update digraph and thus the same dynamical behavior of the network. In this paper we study algorithmical and combinatorial aspects of update digraphs. We show a polynomial characterization of these digraphs, which enables us to characterize the corresponding equivalence classes. We prove that the update digraphs are exactly the projections, on the respective subgraphs, of a complete update digraph with the same number of vertices. Finally, the exact number of complete update digraphs is determined, which provides upper and lower bounds on the number of equivalence classes.