Structural distance and evolutionary relationship of networks
Structural distance and evolutionary relationship of networks
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DOI：
10.1016/j.biosystems.2011.11.004
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发表时间：
2012-03-01
期刊：
影响因子：
1.6
通讯作者：
Banerjee, Anirban
中科院分区：
文献类型：
--
作者：
Banerjee, Anirban
探索生物学和其他领域中一类特定网络的共同特征和普遍性质是进化研究的重要方面之一。在一个进化的系统中，进化机制可以引起功能的变化，迫使系统适应该系统的组件之间的相互作用模式的新配置（例如，基因复制和突变在改变许多生物网络的连接结构中起着至关重要的作用）。两个系统之间的进化关系可以通过它们的结构差异来追溯）。规范化图拉普拉斯算子的特征值不仅捕获网络的全局属性，而且还捕获由图演化（如模体复制或连接）产生的局部结构。该算子的谱承载了图的许多定性方面。给定两个不同规模的网络，提出了一种基于归一化图Laplacian谱对比的拓扑距离量化方法，发现网络结构在同一类内比在类间更相似.我们还表明，进化关系可以追溯的结构差异，使用我们的方法。我们分析了来自不同物种的43个代谢网络，并标记了三个组的显著分离：细菌，古细菌和真核生物。这一现象在我们的研究结果中得到了很好的捕捉，支持了基于基因内容和核糖体RNA序列的其他分支结果。我们的措施，以量化两个网络之间的结构距离是有用的，以阐明进化关系。(C)2011爱思唯尔爱尔兰有限公司保留所有权利。
Exploring common features and universal qualities shared by a particular class of networks in biological and other domains is one of the important aspects of evolutionary study. In an evolving system, evolutionary mechanism can cause functional changes that forces the system to adapt to new configurations of interaction pattern between the components of that system (e.g. gene duplication and mutation play a vital role for changing the connectivity structure in many biological networks. The evolutionary relation between two systems can be retraced by their structural differences). The eigenvalues of the normalized graph Laplacian not only capture the global properties of a network, but also local structures that are produced by graph evolutions (like motif duplication or joining). The spectrum of this operator carries many qualitative aspects of a graph. Given two networks of different sizes, we propose a method to quantify the topological distance between them based on the contrasting spectrum of normalized graph Laplacian.We find that network architectures are more similar within the same class compared to between classes. We also show that the evolutionary relationships can be retraced by the structural differences using our method. We analyze 43 metabolic networks from different species and mark the prominent separation of three groups: Bacteria, Archaea and Eukarya. This phenomenon is well captured in our findings that support the other cladistic results based on gene content and ribosomal RNA sequences. Our measure to quantify the structural distance between two networks is useful to elucidate evolutionary relationships. (C) 2011 Elsevier Ireland Ltd. All rights reserved.