Using VisANT to Analyze Networks

Zhenjun Hu1

1 Bioinformatics Program, Boston University, Boston, Massachusetts
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.8
DOI:  10.1002/0471250953.bi0808s45
Online Posting Date:  March, 2014
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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.

Keywords: interaction; network; meta‐network; visualization; integration

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Basic Network Construction
  • Alternate Protocol 1: Constructing and Comparing Large‐Scale Networks
  • Support Protocol 1: Quantitative Characteristics of Network Topologies
  • Support Protocol 2: Online Saving and Reading of the Network
  • Support Protocol 3: Customizing Visual Properties of the Network
  • Support Protocol 4: Using Batch Mode and Macros
  • Basic Protocol 2: Analyzing the Biological Network
  • Basic Protocol 3: Connecting Genes, Drugs, Diseases, and Therapies: An Application to Drug Repositioning
  • Commentary
  • Figures
     
 
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Materials

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Literature Cited

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Key References
  Hu et al., 2004. See above.
  Introduces the first release of VisANT as an integrative visualization tool for biological networks, with the support of exploratory navigation to walk through interactions based on a few initial genes or proteins of interest.
  Hu et al., 2005. See above.
  Introduces a primary implementation of Metagraph in VisANT to support the integration of context information (such as protein complex, functional modules, etc.) into the network. It also introduces the unique topological analyses (e.g., exhaustive search of shortest paths between two nodes) that are dynamically linked to the network.
  Hu et al., 2007a. See above.
  Introduces details of Metagraph to address the specific features of biological networks.
  Hu et al., 2007b. See above.
  Introduces the Metagraph application in pathway visualization and analysis.
  Hu, Z., Snitkin, E.S., and DeLisi, C. 2008. VisANT: An integrative framework for networks in systems biology. Brief. Bioinform. 9:317‐325.
  Explains the design principals and key development of VisANT system.
  Hu et al., 2009. See above.
  Introduces multi‐scale network visual analysis and inference with integrated Gene Ontology (GO), as well as a sophisticated GO explorer to facilitate the visual navigation and application of GO hierarchy.
  Hu et al., 2013. See above.
  Introduces VisANT's new network‐based cap‐ abilities of translational sciences to convert our understanding of basic biological knowledge into effective ways to treat and prevent diseases, with integrated disease and therapy hierarchies in the Hierarchy Explorer.
Internet Resources
  http://www.visantnet.org
  VisANT homepage.
  http://www.visantnet.org/vmanual
  The VisANT user's manual.
  http://java.sun.com
  Free source of Java run‐time environment 1.4 or above. Refer to VisANT user manual for detailed instruction.
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