Hardy Simon, Robillard Pierre N
Department of Computer Engineering, Ecole Polytechnique de Montréal, P.O. Box 6079, Station Centre-Ville, Montréal, H3C 3A7, Canada.
Bioinformatics. 2008 Jan 15;24(2):209-17. doi: 10.1093/bioinformatics/btm560. Epub 2007 Nov 22.
Cellular signaling networks are dynamic systems that propagate and process information, and, ultimately, cause phenotypical responses. Understanding the circuitry of the information flow in cells is one of the keys to understanding complex cellular processes. The development of computational quantitative models is a promising avenue for attaining this goal. Not only does the analysis of the simulation data based on the concentration variations of biological compounds yields information about systemic state changes, but it is also very helpful for obtaining information about the dynamics of signal propagation.
This article introduces a new method for analyzing the dynamics of signal propagation in signaling pathways using Petri net theory. The method is demonstrated with the Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) regulation network. The results constitute temporal information about signal propagation in the network, a simplified graphical representation of the network and of the signal propagation dynamics and a characterization of some signaling routes as regulation motifs.
细胞信号网络是传播和处理信息并最终引发表型反应的动态系统。理解细胞内信息流的电路是理解复杂细胞过程的关键之一。计算定量模型的发展是实现这一目标的一条有前途的途径。基于生物化合物浓度变化对模拟数据进行分析，不仅能产生有关系统状态变化的信息，而且对于获取信号传播动态的信息也非常有帮助。
本文介绍了一种利用Petri网理论分析信号通路中信号传播动态的新方法。该方法在Ca(2+)/钙调蛋白依赖性蛋白激酶II（CaMKII）调节网络中得到了验证。结果构成了关于网络中信号传播的时间信息、网络及信号传播动态的简化图形表示以及一些作为调节基序的信号传导途径的特征描述。
