Intervention in general topology gene regulatory networks

We present an optimal intervention framework in general topology gene regulatory networks. In particular, we do not make any assumptions about the structure or the connectivity of the initial gene network. The proposed framework finds an optimal perturbation, which forces the network to converge towards a unique desired steady-state distribution. We cast the intervention as an optimization problem, and we show that it admits at most one optimal solution. The existence of the optimal solution depends on the initial network topology and the desired steady-state distribution. In the case where no optimal solution exists, we construct a sequence of suboptimal perturbations, which converge towards a limiting optimal solution. The general topology intervention framework is applied to the Human melanoma gene regulatory network.