Simple tutorial for cytoscape usage

What is cytoscape

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.

How to install cytoscape

• Install Java if you do not have one.

• Download cytoscape.

• App installation

  • Cytoscape menu bar –> Apps –> App manager –> Browse and install apps.
  • 

Simple cytoscape usage

A toy data (saved in toy.txt)

SUPERIOR	SUBORDINATE
Dean	Vice dean1
Dean	Vice dean2
Vice dean1	DirectorA
Vice dean2	DirectorB
Vice dean1	DirectorC
Vice dean1	DirectorD
DirectorA	T1
DirectorA	T2
DirectorB	T3
DirectorB	T4
DirectorB	T5

The toy network

The video tutorial to show how to use cytoscape to transfer the text into a network.

More cytoscape operations

Node searching, adding, deletion, selection and attribute chaning

• Files needed
  • RUAL.subset.sif: Protein-protein interaction data
  • RUAL.subset.na: The map file between Gene ID and protein name
• The video tutorial

• Files needed
  • galFiltered.sif: Protein-protein and protein-DNA interaction data
  • galExpData.mrna: Gene expression profile in various conditions
• Effect picture
  • 

• Time-series expression profile within KEGG pathway

• Files needed
  • KEGG pathway xml file, like ko00900.xml
    • 
  • Expression data for genes involved in ko00900 pathway
• Plugins needed
  • KEGGscape: used to parse XML files of KEGG pathway
  • enhancedGraphics: used to do barPlot and linePlot
• The video tutorial

Import a table to construct network

• Import - Network - File - Selet a two-column file, then a network is constructed.
• Tools - NetworkAnalyzer - Network Analysis - Analyze network, the attribute of the network is analyzed. The analyzing result can be used to set the visualization styles of nodes and edges.

Layout

Attribute Circle Layout is my favorite algorithm to show networks especially when you select some nodes. This algorithm can put nodes with same values together when you are performing Attribute Circle Layout by the related attributes.

For example, I have two classes of genes, one is upregulated, the other is downregulated. This information is saved in a two columns file with the first column containing gene names and the second column named expr containing 0 (down-regulated) and 1 (up-regulated). This file can be imported into Cytoscape by File - Import - Table. Following one can select all these genes and perform Attribute Circle Layout by expr.

Select nodes

Select-Nodes-From ID list file (working in Cytoscape 3.1.1)

Color specific nodes

• Contruct a at-least two columns file to represent nodes and their attributes. Make sure the attribute columns have unique names to facilitate selection.
• Import this attribute file as Node Table Column through FIle - Import - Table.
• Set node color by given attributes using given column names.