<em>cytoHubba</em>: Identify Hub Objects and sub-network from Complex Interactome — ASN Events
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  3. cytoHubba: Identify Hub Objects and sub-network from Complex Interactome

cytoHubba: Identify Hub Objects and sub-network from Complex Interactome (#38)

Chia-Hao Chin 1 , Shu-Hwa Chen 2 , Hsin-Hung Wu 3 , Chin-Wen Ho 4 , Ming-Tat Ko 2 3 , Chung-Yen Lin 2 3 5 6
  1. Department of Computer Science and Information Engineering, Nanhua University, Chiayi, Taiwan
  2. Institute of Information Science, Academia Sinica, Taipei, Taiwan
  3. Research Center of Information Technology Innovation, Academia Sinica, Taipei, Taiwan
  4. Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan
  5. Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
  6. Institute of Fisheries Science, College of Life Science, National Taiwan University, Taipei, Taiwan

Background

Network is a useful tool 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. Itcomputes 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. Cytohubba is available as cytoscape plug-in and can be accessed freely at http://hub.iis.sinica.edu.tw/cytohubba/ for more detail.

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