How to use Cytoscape to analyze coexpression network in ATTED-II

Preparation

• Cytoscape
• Please download the latest Cytoscape from www.cytoscape.org.
• GraphMLReader plugin
• GraphMLReader plugin can be installed using Plugin manager in Cytoscape.
  
  
  
  
• In the Plugin manager, there are lots of plugins, so that please search GraphMLReader by a keyword "graphml".
  After selecting the GraphMLReader, you can install this plugin by clicking "Install" button.
  
  

Import the ATTED-II GraphML file to Cytoscape

In the result page of NetworkDrawer, a link to GraphML file appears. To open the network in Cytoscape, user can simply drag and drop the link of the GraphML file to Cytoscape.



Then pre-layout network will appear. In the default, all of the edges appear, namely, coexpression in All, Tissue, Abiotic, Biotic, Hormone and Light conditions.

Layout the Network on Cytoscape

Cytoscape has many network layout functions. It can be used from Layout in the menu bar.



To know the detail functions of Cytoscape, please visit Cytoscape site (www.cytoscape.org).