UNIT 8.8 Using VisANT to Analyze Networks

Abstract

VisANT is a Web-based workbench for the integrative analysis of biological networks that offers unique features such as exploratory navigation of interaction network and multi-scale visualization and inference with integrated hierarchical knowledge. It provides functionalities for convenient construction, visualization, and analysis of molecular and higher-order networks based on functional (e.g., expression profiles, phylogenetic profiles) and physical (e.g., yeast two-hybrid, chromatin-immunoprecipitation, and drug target) relations from either the Predictome database or user-defined data sets. Analysis capabilities include network structure analysis, over-representation analysis, expression enrichment analysis, etc. Additionally, networks can be saved, accessed, and shared online. VisANT is able to develop and display meta-networks for meta-nodes that are structural complexes, pathways, or any kind of sub-networks. Further, VisANT supports a growing number of standard exchange formats and database-referencing standards, e.g., PSI-MI, KGML, BioPAX, and SBML (in progress). Multiple species are supported to the extent that interactions or associations are available (i.e., public datasets or Predictome database). Curr. Protoc. Bioinform. 45:8.8.1-8.8.39. © 2014 by John Wiley & Sons, Inc.