國家衛生研究院 NHRI:Item 3990099045/8436
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    Please use this identifier to cite or link to this item: http://ir.nhri.org.tw/handle/3990099045/8436


    Title: cytoHubba: Identifying hub objects and sub-networks from complex interactome
    Authors: Chin, CH;Chen, SH;Wu, HH;Ho, CW;Ko, MT;Lin, CY
    Contributors: Division of Biostatistics and Bioinformatics
    Abstract: 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.
    Date: 2014-12-08
    Relation: BMC Systems Biology. 2014 Dec 8;8(Suppl. 4):Article number S11.
    Link to: http://dx.doi.org/10.1186/1752-0509-8-S4-S11
    Cited Times(WOS): https://www.webofscience.com/wos/woscc/full-record/WOS:000346188100012
    Cited Times(Scopus): http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84961596645
    Appears in Collections:[Chung-Yen Lin(1999-2005)] Periodical Articles

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