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

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.

Figure 1

Two screen-shots showing centrality analysis with cytoHubba. (A) A cytoHubba analysis result using the example dataset galFiltered.cys in the Cytoscape. After the calculation (from the Cytoscape menu bar [plugins] → cytoHubba → compute hubba result), top 10 essential nodes ranked by MCC scores were selected (control panel | hubba | → select nodes→ make check on "hubba nodes"→ select a method from "choose a ranking method" and determine how many nodes are selected from "top group" → [submit])from the yeast network. (B) Node and edge annotations are accessible through Cytoscape Data Panel.