Cytoscape is an open source program for visualizing molecular interaction networks and
integrating these interactions with gene expression profiles and other data.
Java Webstart 1.5.0 is required.
The first time you run Cytoscape, Java Webstart automatically downloads and
installs the program on your computer. On subsequent runs, Java Webstart
makes sure your copy of Cytoscape is up-to-date and will download and install a new version if necessary.
Cytoscape is a large program and you should expect a lengthy download the first time you
To operate the program, you specify one or more genes
and click the "Process" button. You can specify
genes by entering identifiers in the text box, uploading a file of gene
identifiers, or choosing an existing gene list from the drop-down menu. The
most reliable gene identifiers are Entrez Gene IDs (e.g., 3630). See Entering Gene Identifiers
for more information.
You can also specify whether to add neighbors.
First neighbors are genes that interact with the genes that you have
specified. Second neighbors are genes that interact with the first
The Cytoscape project is an ongoing collaboration among several institutions and companies. Further information about Cytoscape is available at www.cytoscape.org
. We suggest that you read the Cytoscape tutorial
or User Manual
PDDB creates an
interaction network containing
gene in your input list, neighboring genes if specified, and all interactions
among the input genes and neighbors.
default view is often too crowded to adequately display your network. We
recommend resizing the window, changing the layout to yFiles->Organic, and
clicking the button in the menu bar to "Zoom out to display all of current
Network". To use Cytoscape effectively, we suggest
that you read the Cytoscape tutorial
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