Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome
Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome
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DOI：
10.1093/bioinformatics/17.10.988
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发表时间：
2001-10-01
期刊：
影响因子：
5.8
通讯作者：
Gomez, SM
中科院分区：
文献类型：
--
作者：
Rzhetsky, A;Gomez, SM
动机：基因组学领域的当前增长为基因组中进化机制建模的建模提供了许多令人兴奋的方法。另外，对世界网络等网络的动态和统计分析以及人类之间存在的社交互动，表明这些网络可以表现出常见的分形特性，包括：无标度。这项工作试图桥接这两个领域，并证明分子网络的分形特性与其基本基因组的分形特性相关联。回报：我们建议一个能够描述代谢或信号转导网络进化生长的随机模型。该模型生成的网络与实际分子网络共享重要的统计属性（所谓的无标度行为）。特别是，恰好连接到其他顶点的顶点的频率遵循幂律。分配。该分布的形状仍然存在。网络量表变化不变：一个小的子图具有与从中得出的完整图相同的分布。此外，该模型正确预测不同的DNA和蛋白质结构域的频率也遵循幂律分布。最后，该模型导致一个简单的方程，该方程与基因组中不同DNA和蛋白质结构域的总数均与基因总数和整体网络拓扑结合在一起。
Motivation: Current growth in the field of genomics has provided a number of exciting approaches to the modeling of evolutionary mechanisms within the genome. Separately, dynamical and statistical analyses of networks such as the World Wide Web and the social interactions existing between, humans have shown that these networks can exhibit common fractal properties-including the property of being: scale-free. This work attempts to bridge these two fields, and demonstrate that the fractal properties of molecular networks are linked to the fractal properties of their underlying genomes.Results: We suggest a stochastic model capable of describing the evolutionary growth of metabolic or signal-transduction networks. This model generates networks that share important statistical properties (so-called scale-free behavior) With real molecular networks. In particular, the frequency of vertices, connected to, exactly k other vertices, follows a power-law. distribution. The shape of this distribution remains. invariant to changes in network scale: a small, subgraph has the same distribution as the complete graph from which it is derived. Furthermore, the model correctly predicts that the frequencies of distinct DNA and protein domains also follow a power-law distribution. Finally, the model leads to a simple equation linking the total number of different DNA and protein domains in a genome With both the total number of genes and the overall network topology.