Biological Network Exploration with Cytoscape 3

Gang Su1, John H. Morris2, Barry Demchak3, Gary D. Bader4

1 Molecular Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, 2 Resource for Biocomputing, Visualization, and Informatics, University of California San Francisco, San Francisco, California, 3 Department of Medicine, University of California San Diego, La Jolla, California, 4 The Donnelly Centre, University of Toronto, Toronto
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.13
DOI:  10.1002/0471250953.bi0813s47
Online Posting Date:  September, 2014
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Cytoscape is one of the most popular open‐source software tools for the visual exploration of biomedical networks composed of protein, gene, and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and constructing pathways. Cytoscape provides core functionality to load, visualize, search, filter, and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface, and performance relative to previous versions. This protocol aims to jump‐start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the networks, visualizing network associated data (attributes), and identifying clusters. It also highlights new features that benefit experienced users. Curr. Protoc. Bioinform. 47:8.13.1‐8.13.24. © 2014 by John Wiley & Sons, Inc.

Keywords: Cytoscape; interactive network visualization; network analysis

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Table of Contents

  • Introduction
  • Basic Protocol 1: Analyzing Gene Expression Data in Cytoscape
  • Basic Protocol 2: Explore a Human Disease Network
  • Support Protocol 1: Setting Up Cytoscape
  • Support Protocol 2: Search and Install Apps
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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