Tadaka Shu, Kinoshita Kengo
Graduate School of Information Sciences, Tohoku University, Sendai, Japan.
Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
Bioinformatics. 2016 Nov 15;32(22):3454-3460. doi: 10.1093/bioinformatics/btw488. Epub 2016 Jul 27.
The identification of functional modules from protein-protein interaction (PPI) networks is an important step toward understanding the biological features of PPI networks. The detection of functional modules in PPI networks is often performed by identifying internally densely connected subnetworks, and often produces modules with "core" and "peripheral" proteins. The core proteins are the ones having dense connections to each other in a module. The difference between core and peripheral proteins is important to understand the functional roles of proteins in modules, but there are few methods to explicitly elucidate the internal structure of functional modules at gene level.
We propose NCMine, which is a novel network clustering method and visualization tool for the core-peripheral structure of functional modules. It extracts near-complete subgraphs from networks based on a node-weighting scheme using degree centrality, and reports subgroups as functional modules. We implemented this method as a plugin of Cytoscape, which is widely used to visualize and analyze biological networks. The plugin allows users to extract functional modules from PPI networks and interactively filter modules of interest. We applied the method to human PPI networks, and found several examples with the core-peripheral structure of modules that may be related to cancer development.
The Cytoscape plugin and tutorial are available at Cytoscape AppStore. (http://apps.cytoscape.org/apps/ncmine).
kengo@ecei.tohoku.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.
从蛋白质-蛋白质相互作用（PPI）网络中识别功能模块是理解PPI网络生物学特征的重要一步。在PPI网络中检测功能模块通常是通过识别内部紧密连接的子网来进行的，并且经常会产生具有“核心”和“外围”蛋白质的模块。核心蛋白质是在一个模块中彼此具有紧密连接的那些蛋白质。核心蛋白质和外围蛋白质之间的差异对于理解蛋白质在模块中的功能作用很重要，但很少有方法能够在基因水平上明确阐明功能模块的内部结构。
我们提出了NCMine，它是一种用于功能模块核心-外围结构的新型网络聚类方法和可视化工具。它基于使用度中心性的节点加权方案从网络中提取近乎完整的子图，并将子群报告为功能模块。我们将此方法实现为Cytoscape的一个插件，Cytoscape被广泛用于可视化和分析生物网络。该插件允许用户从PPI网络中提取功能模块并交互式地筛选感兴趣的模块。我们将该方法应用于人类PPI网络，并发现了几个具有可能与癌症发展相关的模块核心-外围结构的例子。
Cytoscape插件和教程可在Cytoscape应用商店获取。（http://apps.cytoscape.org/apps/ncmine）。
kengo@ecei.tohoku.ac.jp补充信息：补充数据可在《生物信息学》在线获取。
