论文标题

布尔网络中的线性切割

Linear cuts in Boolean networks

论文作者

Naldi, Aurélien, Richard, Adrien, Tonello, Elisa

论文摘要

布尔网络是探索生物系统定性动力学特性的流行工具。已经基于相同的逻辑结构提出了几种动态解释,该结构捕获了布尔组件之间的相互作用。他们在不同程度上重现了在更定量的模型中出现的行为。特别是,监管冲突可以防止标准的异步动力学再现一些在检查更详细的模型时可能会预期的轨迹。我们介绍并研究了用线性切割的网络类别,在该类别中,线性组件(与单个调节器和单个目标中间的中间体)消除了上述调节冲突。布尔网络的相互作用图在每个循环中发生线性组件以及从具有多个目标的组件到具有多个调节器的组件时的线性切割。在这种结构条件下,吸引子与最小的陷阱空间一对一地对应,并且吸引子的可达性也很容易被表征。线性切割为布尔语义的新解释提供了基础,该语义捕获了具有调节阈值的多价修补行为,这些行为是针对每种相互作用唯一定义的,并为研究逻辑模型行为的研究提供了新的方法。

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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