UNIT 8.13 Exploring Biological Networks with Cytoscape Software

  1. Natalie Yeung1,
  2. Melissa S. Cline2,
  3. Allan Kuchinsky3,
  4. Michael E. Smoot4,
  5. Gary D. Bader1

Published Online: 1 SEP 2008

DOI: 10.1002/0471250953.bi0813s23

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Yeung, N., Cline, M. S., Kuchinsky, A., Smoot, M. E. and Bader, G. D. 2008. Exploring Biological Networks with Cytoscape Software. Current Protocols in Bioinformatics. 23:8.13:8.13.1–8.13.20.

Author Information

  1. 1

    University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada

  2. 2

    Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California

  3. 3

    Agilent Technologies, Santa Clara, California

  4. 4

    Department of Bioengineering, University of California, San Diego, La Jolla, California

Publication History

  1. Published Online: 1 SEP 2008
  2. Published Print: SEP 2008

This is not the most recent version of the article. View current version (8 SEP 2014)


Cytoscape is a free software package for visualizing, modeling, and analyzing molecular and genetic interaction networks. As a key feature, Cytoscape enables biologists to determine and analyze the interconnectivity of a list of genes or proteins. This unit explains how to use Cytoscape to load and navigate biological network information and view mRNA expression profiles and other functional genomics and proteomics data in the context of the network obtained for genes of interest. Additional analyses that can be performed with Cytoscape are also discussed. Curr. Protoc. Bioinform. 23:8.13.1-8.13.20. © 2008 by John Wiley & Sons, Inc.


  • network visualization;
  • network analysis;
  • systems biology;
  • protein interactions;
  • biological network