title: On the long-run sensitivity of probabilistic Boolean networks.
abstract: Boolean networks and, more generally, probabilistic Boolean networks, as one class of gene regulatory networks, model biological processes with the network dynamics determined by the logic-rule regulatory functions in conjunction with probabilistic parameters involved in network transitions. While there has been significant research on applying different control policies to alter network dynamics as future gene therapeutic intervention, we have seen less work on understanding the sensitivity of network dynamics with respect to perturbations to networks, including regulatory rules and the involved parameters, which is particularly critical for the design of intervention strategies. This paper studies this less investigated issue of network sensitivity in the long run. As the underlying model of probabilistic Boolean networks is a finite Markov chain, we define the network sensitivity based on the steady-state distributions of probabilistic Boolean networks and call it long-run sensitivity. The steady-state distribution reflects the long-run behavior of the network and it can give insight into the dynamics or momentum existing in a system. The change of steady-state distribution caused by possible perturbations is the key measure for intervention. This newly defined long-run sensitivity can provide insight on both network inference and intervention. We show the results for probabilistic Boolean networks generated from random Boolean networks and the results from two real biological networks illustrate preliminary applications of sensitivity in intervention for practical problems.
authors.affiliation: Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA. xqian@tamu.edu
authors.forename: Xiaoning
authors.initials: X
authors.lastname: Qian
authors.forename: Edward R
authors.initials: ER
authors.lastname: Dougherty
mesh_terms: D000818:Animals; D002453:Cell Cycle / Q000235:genetics; D005786:Gene Expression Regulation; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D018816:Genes, cdc; D006801:Humans; D008322:Mammals / Q000235:genetics; D008390:Markov Chains; D008545:Melanoma / Q000235:genetics / Q000556:secondary; D008957:Models, Genetic; D011336:Probability