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

Chia Hao Chin, Shu Hwa Chen, Hsin Hung Wu, Chin Wen Ho, Ming Tat Ko, Chung Yen Lin

Research output: Contribution to journalArticle

390 Citations (Scopus)

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.

Original languageEnglish
Article numberS11
JournalBMC Systems Biology
Volume8
Issue number4
DOIs
Publication statusPublished - Dec 8 2014
Externally publishedYes

ASJC Scopus subject areas

  • Structural Biology
  • Modelling and Simulation
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Fingerprint Dive into the research topics of 'cytoHubba: Identifying hub objects and sub-networks from complex interactome'. Together they form a unique fingerprint.

  • Cite this