Miryala Sravan Kumar, Anbarasu Anand, Ramaiah Sudha
Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India.
Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India.
Gene. 2018 Feb 5;642:84-94. doi: 10.1016/j.gene.2017.11.028. Epub 2017 Nov 10.
Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks.
生物分子相互作用网络的计算分析对于理解新基因/蛋白质的功能正变得越来越重要。基因相互作用（GI）网络分析和蛋白质-蛋白质相互作用（PPI）网络分析在预测相互作用基因或蛋白质的功能方面发挥着重要作用，并能深入了解基因间相互作用的功能关系和进化保守性。相互作用网络是基因/蛋白质相互作用组的图形表示，其中每个基因/蛋白质是一个节点，基因/蛋白质之间的相互作用是一条边。在这篇综述中，我们讨论了作为数据存储库用于搜索和收集蛋白质/基因相互作用数据的流行开源数据库，以及可用于生成相互作用网络、可视化和网络分析的工具。此外，还讨论了各种网络分析方法，如用于研究网络特性的拓扑方法和聚类方法，以及用于阐明基因和蛋白质功能及途径的功能富集服务器。因此，本综述中提到的独特之处不仅在于提供基因和蛋白质-蛋白质相互作用（PPI）网络分析的工具和网络服务器概述，还在于从相互作用网络中提取有用且有意义的信息。
