cytoHubba: identifying hub objects and sub-networks from complex interactome.
cytoHubba: identifying hub objects and sub-networks from complex interactome.
复制标题
DOI：
10.1186/1752-0509-8-s4-s11
复制
发表时间：
2014
影响因子：
--
通讯作者：
Lin CY
中科院分区：
文献类型：
--
作者：
Chin CH;Chen SH;Wu HH;Ho CW;Ko MT;Lin CY
网络是一种有用的方式来呈现许多类型的生物数据，包括蛋白质-蛋白质相互作用，基因调控，细胞通路和信号转导。我们可以通过节点的网络特征来衡量它们在网络中的重要性，它可以帮助我们识别生物网络的中心元素。我们引入了一个新的Cytoscape插件cytoHubba，用于通过网络特征对网络中的节点进行排名。CytoHubba提供了11种拓扑分析方法，包括度，边缘渗透分量，最大邻域分量，最大邻域分量密度，最大团中心性和基于最短路径的六个中心性（瓶颈，偏心，接近度，辐射度，介数和应力）。在这11种方法中，新提出的方法MCC在酵母PPI网络预测必需蛋白质的精度上具有更好的性能。CytoHubba提供了一个用户友好的界面来探索生物网络中的重要节点。它以一站式购物的方式计算所有11种方法。此外，研究人员能够将联合收割机cytoHubba与其他插件结合成一个新的分析方案。通过这种拓扑分析策略捕获的网络和子网络将为实验生物学家带来对基本调控网络和蛋白质药物靶点的新见解。根据cytoscape插件下载统计，自2010年以来，cytoHubba的累计次数约为6,700次。
Network is a useful way for presenting many types of biological data including protein-protein interactions, gene regulations, cellular pathways, and signal transductions. We can measure nodes by their network features to infer their importance in the network, and it can help us identify central elements of biological networks. We introduce a novel Cytoscape plugin cytoHubba for ranking nodes in a network by their network features. CytoHubba provides 11 topological analysis methods including Degree, Edge Percolated Component, Maximum Neighborhood Component, Density of Maximum Neighborhood Component, Maximal Clique Centrality and six centralities (Bottleneck, EcCentricity, Closeness, Radiality, Betweenness, and Stress) based on shortest paths. Among the eleven methods, the new proposed method, MCC, has a better performance on the precision of predicting essential proteins from the yeast PPI network. CytoHubba provide a user-friendly interface to explore important nodes in biological networks. It computes all eleven methods in one stop shopping way. Besides, researchers are able to combine cytoHubba with and other plugins into a novel analysis scheme. The network and sub-networks caught by this topological analysis strategy will lead to new insights on essential regulatory networks and protein drug targets for experimental biologists. According to cytoscape plugin download statistics, the accumulated number of cytoHubba is around 6,700 times since 2010.