基于图匹配的蛋白质-蛋白质相互作用网络的全局比对
Global alignment of protein-protein interaction networks by graph matching methods
摘要：
排列不同物种的蛋白质-蛋白质相互作用（PPI）网络最近引起了相当大的兴趣。这个问题对于研究物种间进化保守的途径或蛋白质复合物，以及通过检测保守的相互作用来帮助鉴定功能性直系同源物是重要的。然而，这是一个困难的组合问题，只有启发式方法已提出到目前为止。我们重新制定的PPI对齐作为一个图形匹配问题，并研究如何国家的最先进的图形匹配算法可以用于此目的。我们区分两个比对问题，这取决于是否严格限制蛋白质匹配，基于序列相似性，或者目标是找到一个最佳的折衷序列相似性和相互作用之间的保守性的比对。我们提出了新的方法，这两种情况下，并评估其性能的酵母和苍蝇PPI网络的对齐。新方法始终优于最先进的算法，特别是在给定的序列相似性水平下，检索比IsoRank多78%的保守相互作用。可用性：http：//cbio.ensmp.fr/proj/graphm\_graphm/，可根据要求提供其他数据和代码。联系人：jean-philippe. mines-paristech.fr
英文摘要：
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help in the identification of functional orthologs through the detection of conserved interactions. It is however a difficult combinatorial problem, for which only heuristic methods have been proposed so far. We reformulate the PPI alignment as a graph matching problem, and investigate how state-of-the-art graph matching algorithms can be used for that purpose. We differentiate between two alignment problems, depending on whether strict constraints on protein matches are given, based on sequence similarity, or whether the goal is instead to find an optimal compromise between sequence similarity and interaction conservation in the alignment. We propose new methods for both cases, and assess their performance on the alignment of the yeast and fly PPI networks. The new methods consistently outperform state-of-the-art algorithms, retrieving in particular 78% more conserved interactions than IsoRank for a given level of sequence similarity. Availability:http://cbio.ensmp.fr/proj/graphm\_ppi/, additional data and codes are available upon request. Contact: jean-philippe.vert@mines-paristech.fr
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