布尔网络中的线性割
Linear cuts in Boolean networks
摘要：
布尔网络是探索生物系统定性动力学性质的常用工具。已经提出了几个动态的解释，基于相同的逻辑结构，捕捉布尔组件之间的相互作用。它们在不同程度上再现了更多量化模型中出现的行为。特别是，监管冲突可以防止标准的异步动态复制一些轨迹，可能是预期在检查更详细的模型。我们介绍和研究一类网络与线性切割，线性组件-一个单一的监管机构和一个单一的目标-消除上述监管冲突的中间体。布尔网络的相互作用图允许线性切割时，线性组件发生在每个周期和每个路径从组件与多个目标组件与多个调节器。在这种结构条件下，吸引子与最小陷阱空间一一对应，吸引子的可达性也可以很容易地刻画。线性切割提供了一个新的解释的布尔语义，捕捉所有的行为的多值细化与监管阈值，是唯一定义的每个互动的基础，并有助于一个新的方法，调查行为的逻辑模型。
英文摘要：
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions between Boolean components. They reproduce, in different degrees, the behaviours emerging in more quantitative models. In particular, regulatory conflicts can prevent the standard asynchronous dynamics from reproducing some trajectories that might be expected upon inspection of more detailed models. We introduce and study the class of networks with linear cuts, where linear components -- intermediates with a single regulator and a single target -- eliminate the aforementioned regulatory conflicts. The interaction graph of a Boolean network admits a linear cut when a linear component occurs in each cycle and in each path from components with multiple targets to components with multiple regulators. Under this structural condition the attractors are in one-to-one correspondence with the minimal trap spaces, and the reachability of attractors can also be easily characterized. Linear cuts provide the base for a new interpretation of the Boolean semantics that captures all behaviours of multi-valued refinements with regulatory thresholds that are uniquely defined for each interaction, and contribute a new approach for the investigation of behaviour of logical models.
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