Using the Contextual Hub Analysis Tool (CHAT) in Cytoscape to Identify Contextually Relevant Network Hubs

Tanja Muetze1, David J. Lynn2

1 EMBL Australia Biomedical Informatics Group, Infection & Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, 2 School of Medicine, Flinders University, Bedford Park
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.24
DOI:  10.1002/cpbi.35
Online Posting Date:  September, 2017
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Abstract

Highly connected nodes in biological networks are called network hubs. Hubs are topologically important to the structure of the network and have been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we provide a step‐by‐step protocol for using the Contextual Hub Analysis Tool (CHAT), an application within Cytoscape 3, which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene or protein expression data, and identify hub nodes that are more highly connected to contextual nodes than expected by chance. © 2017 by John Wiley & Sons, Inc.

Keywords: CHAT; contextual hub analysis; gene expression; network analysis; Cytoscape 3

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Installing, Launching, and Using CHAT
  • Support Protocol 1: Installation of Java 8+ and Cytoscape 3.0+
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Installing, Launching, and Using CHAT

  Materials
  • A modern Web browser, such as Chrome, Safari, or Firefox
  • A (high‐speed) Internet connection
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Figures

Videos

Literature Cited

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Internet Resources
  http://apps.cytoscape.org/apps/chat
  CHAT software.
  https://bitbucket.org/dynetteam/chat
  Latest CHAT source code.
  https://bitbucket.org/dynetteam/chat/downloads
  CHAT downloads. License: Lesser GNU Public License 3.0.
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