View Human Affymetrix gene expression data on Cancer Cell Map pathways in 3 easy steps
- Click to start the Expression Viewer software (requires Java Web Start)
- Select the Cancer Cell Map pathway you want to view
- Load your Human Affymetrix gene expression data. Note: this requires your data to conform to a specific, but easy to create format. See a sample (right click to download and be sure to save with .pvals extension).
More details...
Screenshot
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| (photo depicts Cytoscape running with the Expression Viewer Plugin. The KitReceptor pathway has been loaded and overlaid with expression data. Red circles represent highly upregulated genes - an indication of unusually high mRNA levels) |
About the Cytoscape and the Expression Viewer Cytoscape Plugin
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. (Find out more at: cytoscape.org). Cytoscape includes a built-in plugin framework for adding new features and functionality. The Expression Viewer plugin enables Cytoscape users to visualize expression data in the context of cPath Pathways.Note: The Expression Viewer plugin currently only works with Cytoscape 2.2, or later. It will not work with earlier versions of Cytoscape.
Bugs / Feature Requests
If you encounter a bug with this PlugIn, or have a feature suggestion, we encourage you to use the Cytoscape Bug Tracker.If you log a bug, we will automatically email you when the bug is resolved.
Contacts
Sander Group, Computational Biology Center
Memorial Sloan-Kettering Cancer Center, New York City
For any questions concerning this PlugIn, please contact:
This software is made available under the LGPL (Lesser General Public License).
This product includes software developed by the Apache Software Foundation