拓扑网络比对揭示生物学功能和遗传
Topological network alignment uncovers biological function and phylogeny
摘要：
序列比较和比对对我们理解进化、生物学和疾病产生了巨大的影响。生物网络的比较和排列可能会产生类似的影响。现有的网络比对使用网络外部的信息，例如序列，因为还没有设计出用于纯拓扑比对的好算法。在本文中，我们提出了一种新的算法，完全基于网络拓扑结构，可以用来对齐任何两个网络。我们将其应用于生物网络，以产生迄今为止最完整的生物网络拓扑对齐。我们证明，物种的遗传学和详细的生物功能的个别蛋白质可以从我们的比对提取。基于拓扑的比对有可能提供一个全新的、独立的系统发育信息来源。我们对两个非常不同的物种--酵母和人类--的蛋白质相互作用网络的比对表明，即使是遥远的物种，彼此之间也有惊人的网络拓扑结构，这表明地球上所有生命的内部细胞布线具有广泛的相似性。
英文摘要：
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments. Topology-based alignments have the potential to provide a completely new, independent source of phylogenetic information. Our alignment of the protein-protein interaction networks of two very different species--yeast and human--indicate that even distant species share a surprising amount of network topology with each other, suggesting broad similarities in internal cellular wiring across all life on Earth.
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