Computing topological parameters of biological networks

TLDR

Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. The authors developed the Cytoscape plugin NetworkAnalyzer to gain insight into the organization and structure of the large complex networks formed by interacting molecules. NetworkAnalyzer computes and displays a comprehensive set of topological parameters—including node and edge counts, connected components, diameter, radius, density, centralization, heterogeneity, clustering coefficient, characteristic path length, and degree and connectivity distributions—while supporting directed and undirected networks, allowing construction of network intersections or unions, and providing an interactive, customizable interface that does not require graph theory expertise. NetworkAnalyzer is available for download from the Cytoscape website (http://www.cytoscape.org); supplementary data can be accessed online and contact is [e-mail].

Abstract

Abstract Summary: Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. In order to gain insight into the organization and structure of the resultant large complex networks formed by the interacting molecules, we have developed the versatile Cytoscape plugin NetworkAnalyzer. It computes and displays a comprehensive set of topological parameters, which includes the number of nodes, edges, and connected components, the network diameter, radius, density, centralization, heterogeneity, and clustering coefficient, the characteristic path length, and the distributions of node degrees, neighborhood connectivities, average clustering coefficients, and shortest path lengths. NetworkAnalyzer can be applied to both directed and undirected networks and also contains extra functionality to construct the intersection or union of two networks. It is an interactive and highly customizable application that requires no expert knowledge in graph theory from the user. Availability: NetworkAnalyzer can be downloaded via the Cytoscape web site: http://www.cytoscape.org Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.