Cytoscape教程(一)
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鈩?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.
https://v.qq.com/txp/iframe/player.html?vid=e050243v8ol&width=500&height=375&auto=0
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
https://v.qq.com/txp/iframe/player.html?vid=o05022bnnv3&width=500&height=375&auto=0
Heatmap nodes color using expression data
Files needed
galFiltered.sif: Protein-protein and protein-DNA interaction data
galExpData.mrna: Gene expression profile in various conditions
Effect picture
http://v.qq.com/x/page/h0502n2uvqw.html
Cytoscape mapping gene expression to KEGG pathway
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
https://v.qq.com/txp/iframe/player.html?vid=h0502wze2tq&width=500&height=375&auto=0
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
throughFIle
-Import
-Table
.Set node color by given attributes using given column names.