cytoHubba: identifying hub objects and sub-networks from complex interactome

被引:4325
作者
Chin, Chia-Hao [1 ]
Chen, Shu-Hwa [2 ]
Wu, Hsin-Hung [6 ]
Ho, Chin-Wen [5 ]
Ko, Ming-Tat [2 ,6 ]
Lin, Chung-Yen [2 ,3 ,4 ]
机构
[1] Nanhua Univ, Dept Comp Sci & Informat Engn, Dalin Township 62249, Chiayi County, Taiwan
[2] Acad Sinica, Inst Informat Sci, Taipei 115, Taiwan
[3] Natl Hlth Res Inst, Inst Populat Hlth Sci, Div Biostat & Bioinformat, Zhunan 350, Taiwan
[4] Natl Taiwan Univ, Inst Fisheries Sci, Coll Life Sci, Taipei 105, Taiwan
[5] Natl Cent Univ, Dept Comp Sci & Informat Engn, Taoyuan 320, Taiwan
[6] Acad Sinica, Res Ctr Informat Technol Innovat, Taipei 115, Taiwan
来源
BMC SYSTEMS BIOLOGY | 2014年 / 8卷
关键词
CENTRALITY; PARAMETERS;
D O I
10.1186/1752-0509-8-S4-S11
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Background: 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. Results: 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. Conclusions: 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.
引用
收藏
页数:7
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