Maximum Number of Fixed Points in Regulatory Boolean Networks

Departamento Ingeniería Matemática, Universidad de Concepción, Av. Esteban Iturra s/n, Casilla 160-C, Concepción, Chile.
Bulletin of Mathematical Biology (Impact Factor: 1.39). 08/2008; 70(5):1398-409. DOI: 10.1007/s11538-008-9304-7
Source: PubMed


Boolean networks (BNs) have been extensively used as mathematical models of genetic regulatory networks. The number of fixed points of a BN is a key feature of its dynamical behavior. Here, we study the maximum number of fixed points in a particular class of BNs called regulatory Boolean networks, where each interaction between the elements of the network is either an activation or an inhibition. We find relationships between the positive and negative cycles of the interaction graph and the number of fixed points of the network. As our main result, we exhibit an upper bound for the number of fixed points in terms of minimum cardinality of a set of vertices meeting all positive cycles of the network, which can be applied in the design of genetic regulatory networks.

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    • "In Information Theory, the study of fix(G, F) is strongly related to the network coding solvability problem [17] [5], and here again upper-bound are of special interest. It is then not so surprising that the following fundamental bound has been established independently in both contexts [3] [2] [17]: For every digraph G, "
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    ABSTRACT: For a graph $G$, let $\mathcal{C}$ be the set of conjunctive networks with interaction graph $G$, and let $\mathcal{H}$ be the set of graphs obtained from $G$ by contracting some edges. Let $\mathrm{fix}(f)$ be the number of fixed points in a network $f\in \mathcal{C}$, and let $\mathrm{mis}(H)$ be the number of maximal independent sets in $H\in\mathcal{H}$. Our main result is \[\mathrm{mis}(G)~\leq~\max_{H\in\mathcal{H}}\mathrm{mis}(H)~\leq~ \max_{f\in\mathcal{C}}\mathrm{fix}(f)~\leq~ \left(\frac{3}{2}\right)^{m(G)}\mathrm{mis}(G) \] where $m(G)$ is the maximum size of a matching $M$ of $G$ such that every edge of $M$ is contained in an induced copy of $C_4$ that contains no other edge of $M$. Thus if $G$ has no induced $C_4$ then $\max_{H\in\mathcal{H}}\mathrm{mis}(H)=\max_{f\in\mathcal{C}}\mathrm{fix}(f)=\mathrm{mis}(G)$, and this contrasts with following complexity result: It is coNP-hard to decide if $\max_{f\in\mathcal{C}}\mathrm{fix}(f)=\mathrm{mis}(G)$ or if $\max_{H\in\mathcal{H}}\mathrm{mis}(H)=\mathrm{mis}(G)$, even if $G$ has a unique induced copy of $C_4$.
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    • "positive) cycles, then every boolean G-function has no fixed points (resp. at least two fixed points) and is thus not nilpotent [1]. These observations lead us to study the unsigned version of the question, which is more tractable. "
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    Preview · Article · Mar 2015
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    • "For instance, the min-net introduced in Section II-C is a non-decreasing coding function. Non-decreasing coding functions have been widely studied (see [25], [29], [28]); they are usually represented by an interaction graph with positive signs on all arcs (see [29] and the references therein for a survey of the work on signed interaction graphs). "
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