Title :
Design of Boolean networks based on prescribed singleton attractors
Author :
Kobayashi, Kaoru ; Hiraishi, Kunihiko
Author_Institution :
Sch. of Inf. Sci., Japan Adv. Inst. of Sci. & Technol., Ishikawa, Japan
Abstract :
Attractors in gene regulatory networks represent cell types or states of cells. In system biology and synthetic biology, it is important to generate gene regulatory networks with desired attractors. In this paper, we focus on a singleton attractor, which is also called a fixed point. Using a Boolean network (BN) model, we consider the problem of finding Boolean functions such that the system has desired singleton attractors and has no undesired singleton attractors. To solve this problem, we propose a matrix-based representation of BNs. Using this representation, the problem of finding Boolean functions can be rewritten as an integer linear programming problem. Furthermore, the effectiveness of the proposed method is shown by a numerical example on a WNT5A network, which is related to melanoma. The proposed method provides us a basic method for design of gene regulatory networks.
Keywords :
Boolean functions; biology; integer programming; linear programming; matrix algebra; network theory (graphs); BN; Boolean functions; Boolean network design; WNT5A network; cell states; cell types; gene regulatory networks; integer linear programming problem; matrix-based representation; melanoma; prescribed singleton attractors; synthetic biology; system biology; Boolean functions; Gold; Indexes; Mathematical model; Nickel; Systems biology; Vectors;
Conference_Titel :
Control Conference (ECC), 2014 European
Conference_Location :
Strasbourg
Print_ISBN :
978-3-9524269-1-3
DOI :
10.1109/ECC.2014.6862342