Design of Boolean networks based on prescribed singleton attractors
Design of Boolean networks based on prescribed singleton attractors
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DOI：
10.1109/ecc.2014.6862342
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发表时间：
2014-06
期刊：
影响因子：
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通讯作者：
Koichi Kobayashi;K. Hiraishi
中科院分区：
文献类型：
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作者：
Koichi Kobayashi;K. Hiraishi
基因调控网络中的吸引子代表细胞类型或细胞状态。在系统生物学和合成生物学中，重要的是生成具有期望吸引子的基因调控网络。在这篇文章中，我们关注的是单点吸引子，也被称为不动点。利用布尔网络（BN）模型，我们考虑的问题，找到布尔函数，使系统具有期望的单点吸引子，没有不需要的单点吸引子。为了解决这个问题，我们提出了一个基于矩阵的表示BN。使用这种表示，寻找布尔函数的问题可以重写为整数线性规划问题。最后，通过一个与黑色素瘤相关的WNT5A网络的数值算例，验证了该方法的有效性。该方法为基因调控网络的设计提供了一种基本方法。
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.