Cytoscape is an open source software platform for visualizing molecularinteraction networks and biological pathways and integrating thesenetworks with annotations, gene expression profiles and other statedata. Although Cytoscape was originally designed for biologicalresearch, now it is a general platform for complex network analysisand visualization. Cytoscape core distribution provides a basic setof 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, andconnection with databases. They may be developed by anyone usingthe Cytoscape open API based on Java鈩?technology and Appcommunity development is encouraged. Most of the Apps are freelyavailable from Cytoscape App Store.
Install Java if you do not have one.
Download cytoscape.
App installation
Cytoscape menu bar → Apps → App manager → Browse and install apps.
A toy data (saved in toy.txt
)
SUPERIOR SUBORDINATEDean Vice dean1Dean Vice dean2Vice dean1 DirectorAVice dean2 DirectorBVice dean1 DirectorCVice dean1 DirectorDDirectorA T1DirectorA T2DirectorB T3DirectorB T4DirectorB T5
The toy network
The video tutorial to show how to use cytoscape
to transfer the textinto a network.
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
//v.qq.com/x/page/h0502n2uvqw.html
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
- 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.
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 areperforming 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 CircleLayout
by expr
.
Select
-Nodes
-From ID list file
(working in Cytoscape 3.1.1)
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.
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