Using VisANT to Analyze Networks

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.