Department of Physics, Koç University, Sariyer 34450 Istanbul, Turkey.
J Theor Biol. 2010 Apr 7;263(3):328-36. doi: 10.1016/j.jtbi.2009.12.008. Epub 2009 Dec 22.
We investigate the structural and dynamical properties of the transcriptional regulatory network of the Yeast Saccharomyces cerevisiae and compare it with two "unbiased" ensembles: one obtained by reshuffling the edges and the other generated by mimicking the transcriptional regulation mechanism within the cell. Both ensembles reproduce the degree distributions (the first-by construction-exactly and the second approximately), degree-degree correlations and the k-core structure observed in Yeast. An exceptionally large dynamically relevant core network found in Yeast in comparison with the second ensemble points to a strong bias towards a collective organization which is achieved by subtle modifications in the network's degree distributions. We use a Boolean model of regulatory dynamics with various classes of update functions to represent in vivo regulatory interactions. We find that the Yeast's core network has a qualitatively different behavior, accommodating on average multiple attractors unlike typical members of both reference ensembles which converge to a single dominant attractor. Finally, we investigate the robustness of the networks and find that the stability depends strongly on the used function class. The robustness measure is squeezed into a narrower band around the order-chaos boundary when Boolean inputs are required to be nonredundant on each node. However, the difference between the reference models and the Yeast's core is marginal, suggesting that the dynamically stable network elements are located mostly on the peripherals of the regulatory network. Consistently, the statistically significant three-node motifs in the dynamical core of Yeast turn out to be different from and less stable than those found in the full transcriptional regulatory network.
我们研究了酵母酿酒酵母转录调控网络的结构和动力学性质，并将其与两个“无偏”集合进行了比较：一个通过重新排列边缘获得，另一个通过模拟细胞内转录调控机制生成。这两个集合都再现了酵母中观察到的度分布（第一个通过构造完全，第二个大约）、度-度相关性和 k-核结构。与第二个集合相比，酵母中发现的一个异常大的动态相关核心网络表明存在强烈的集体组织偏向，这是通过网络度分布的微妙修改实现的。我们使用具有各种更新函数类的调节动力学布尔模型来表示体内调节相互作用。我们发现，酵母的核心网络具有不同的定性行为，能够平均容纳多个吸引子，而不是典型的参考集合成员，它们都收敛到一个单一的主导吸引子。最后，我们研究了网络的鲁棒性，发现稳定性强烈依赖于使用的函数类。当布尔输入在每个节点上都需要是非冗余的时，稳定性度量被挤压到接近有序-混沌边界的较窄带宽内。然而，参考模型和酵母核心之间的差异很小，这表明动态稳定的网络元素主要位于调节网络的外围。一致地，酵母动态核心中的统计显著三节点模式与在完整转录调节网络中发现的模式不同，并且不太稳定。
