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Front Physiol. 2018 May 8;9:454. doi: 10.3389/fphys.2018.00454. eCollection 2018.

Target Control in Logical Models Using the Domain of Influence of Nodes.

Author information

1
Department of Physics, Pennsylvania State University, University Park, PA, United States.
2
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States.
3
Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, United States.
4
Department of Biology, Pennsylvania State University, University Park, PA, United States.

Abstract

Dynamical models of biomolecular networks are successfully used to understand the mechanisms underlying complex diseases and to design therapeutic strategies. Network control and its special case of target control, is a promising avenue toward developing disease therapies. In target control it is assumed that a small subset of nodes is most relevant to the system's state and the goal is to drive the target nodes into their desired states. An example of target control would be driving a cell to commit to apoptosis (programmed cell death). From the experimental perspective, gene knockout, pharmacological inhibition of proteins, and providing sustained external signals are among practical intervention techniques. We identify methodologies to use the stabilizing effect of sustained interventions for target control in Boolean network models of biomolecular networks. Specifically, we define the domain of influence (DOI) of a node (in a certain state) to be the nodes (and their corresponding states) that will be ultimately stabilized by the sustained state of this node regardless of the initial state of the system. We also define the related concept of the logical domain of influence (LDOI) of a node, and develop an algorithm for its identification using an auxiliary network that incorporates the regulatory logic. This way a solution to the target control problem is a set of nodes whose DOI can cover the desired target node states. We perform greedy randomized adaptive search in node state space to find such solutions. We apply our strategy to in silico biological network models of real systems to demonstrate its effectiveness.

KEYWORDS:

Boolean network; biological network; domain of influence; logical modeling; network dynamics; target control

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