论文标题
关于拓扑驱动的生物网络的当前失败(但光明的未来)
On the current failure -- but bright future -- of topology-driven biological network alignment
论文作者
论文摘要
蛋白质的功能由其相互作用伙伴定义。因此,两个物种的蛋白质 - 蛋白质相互作用(PPI)网络的拓扑驱动的网络比对应发现相似的相互作用模式,并允许鉴定功能相似的蛋白质。霍弗(Howver),PPI网络对齐的五十个或更多算法中很少有网络拓扑与功能相似性之间存在着重要的联系,并且仅使用网络拓扑结构恢复了直系同源物。我们发现,导致该故障的主要因素是:(i)当前PPI网络中的边缘密度太低,无法期望拓扑网络对齐能够成功; (ii)当边缘密度足够高时,拓扑相似性的某些度量很容易在功能上相似,而其他蛋白质则不太相似; (iii)大多数网络对齐算法无法优化其自己的拓扑目标功能,从而阻碍了它们有效使用拓扑的能力。我们证明,SANA(模拟的退火网络对齐器对准器都非常明显地优于现有的对准器,可以优化其自己的目标函数,甚至在已知最佳解决方案时就可以实现近乎最佳的解决方案。我们提供了仅基于拓扑的全球网络对齐的首次演示,仅在某些情况下,在1E-300以下的情况下,在功能上相似的蛋白质与P值相似。我们预测,随着边缘密度朝着良好对齐的价值增长,拓扑网络对齐将具有光明的未来。我们证明,当在近期的集成互动数据库 - 流动网络对齐的最近部分合成网络中,在足够高的边缘密度上存在足够的共同拓扑,很容易恢复大多数源源直源,从而铺平了基于拓扑驱动网络的高通量功能预测的方式。
The function of a protein is defined by its interaction partners. Thus, topology-driven network alignment of the protein-protein interaction (PPI) networks of two species should uncover similar interaction patterns and allow identification of functionally similar proteins. Howver, few of the fifty or more algorithms for PPI network alignment have demonstrated a significant link between network topology and functional similarity, and none have recovered orthologs using network topology alone. We find that the major contributing factors to this failure are: (i) edge densities in current PPI networks are too low to expect topological network alignment to succeed; (ii) when edge densities are high enough, some measures of topological similarity easily uncover functionally similar proteins while others do not; and (iii) most network alignment algorithms fail to optimize their own topological objective functions, hampering their ability to use topology effectively. We demonstrate that SANA-the Simulated Annealing Network Aligner-significantly outperforms existing aligners at optimizing their own objective functions, even achieving near-optimal solutions when optimal solution is known. We offer the first demonstration of global network alignments based on topology alone that align functionally similar proteins with p-values in some cases below 1e-300. We predict that topological network alignment has a bright future as edge densities increase towards the value where good alignments become possible. We demonstrate that when enough common topology is present at high enough edge densities-for example in the recent, partly synthetic networks of the Integrated Interaction Database-topological network alignment easily recovers most orthologs, paving the way towards high-throughput functional prediction based on topology-driven network alignment.