Unit

UNIT 8.8 Analyzing Networks with VisANT

  1. Zhenjun Hu,
  2. Joseph Mellor,
  3. Charles DeLisi

Published Online: 1 DEC 2004

DOI: 10.1002/0471250953.bi0808s08

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Hu, Z., Mellor, J. and DeLisi, C. 2004. Analyzing Networks with VisANT. Current Protocols in Bioinformatics. 8:8.8:8.8.1–8.8.24.

Author Information

  1. Boston University, Boston, Massachusetts

Publication History

  1. Published Online: 1 DEC 2004
  2. Published Print: NOV 2004

This is not the most recent version of the article. View current version (21 MAR 2014)

Abstract

The VisANT tool, accessible from any recent Java-enabled browser, is a platform-independent, flexible, Web-enabled program for quick and simple 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) relations from either the Predictome database or user-defined data sets. Analysis capabilities include identification of feed-forward and -back loops, shortest paths, and node degree distribution. Additionally, network constructs can be saved, accessed, and shared online. VisANT is able to develop and display meta-networks for meta-nodes that are structural complexes or pathways (soon including nodes representing any kind of dense cluster). Further, VisANT supports a growing number of standard exchange formats and database referencing standards, e.g., KEGG/KGML, BioPAX (in progress), GenBank, Gene Ontology. Multiple species are supported to the extent that computed or experimental evidence of interactions or associations are available (i.e., public datasets or Predictome database).

Keywords:

  • interaction;
  • network;
  • meta-network;
  • visualization;
  • integration