GeneMANIA Cytoscape Plugin

The GeneMANIA Cytoscape plugin brings fast gene function prediction capabilities to the desktop. GeneMANIA identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses a large database of functional interaction networks from multiple organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data. The plugin follows the look and feel of the GeneMANIA website, but provides more features for power-users:

  • Number of query genes is limited only by the amount of memory available
  • Powerful command line tools to automate basic and advanced analysis not available via the website
  • Users can add their own organisms
  • Integration with the popular Cytoscape network visualization and analysis platform so Cytoscape networks can be imported into GeneMANIA and GeneMANIA results can be used in other Cytoscape analysis. Also, results can be saved in Cytoscape session files for later work, backup or sharing with colleagues.

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.
Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD (2010)
Bioinformatics 26: 22.
Full Article (PDF)

Minimum System Requirements

  • Java 1.5+ JVM (1.6 is required for Cytoscape 2.8+)
    Note: Queries that use more than 1.5 GB of RAM require Cytoscape to be launched with a 64-bit JVM
  • Cytoscape 2.6.3+, 2.7+, or 2.8+ (does not work with 3.0 yet)
  • 2 GB RAM

Installation Instructions

  1. Adjust the amount of memory allocated to Cytoscape to at least 1.5GB
  2. In Cytoscape, go to Plugins » Manage Plugins.
  3. Under Available for Install » Network Inference, select GeneMANIA.
  4. Click Install.

Development Snapshot Installation Instructions

Note: If you have already installed an official GeneMANIA release, you need to remove it before you can install a development snapshot.

  1. Adjust the amount of memory allocated to Cytoscape to at least 1.5GB
  2. In Cytoscape, go to Plugins » Manage Plugins.
  3. Click Change Download Site.
  4. Click Edit Sites.
  5. Click Add.
  6. Under Name, type: GeneMANIA.
  7. Under URL, type: http://www.genemania.org/plugin/plugins-dev.xml.
  8. Click Ok until you get back to the plugin selection page.
  9. Under Available for Install » Network Inference, select GeneMANIA.
  10. Click Install.

GeneMANIA is actively developed at the University of Toronto, in the Donnelly Centre for Cellular and Biomolecular Research, in the labs of Gary Bader and Quaid Morris, with input from an independent scientific advisory board. GeneMANIA development is funded by Genome Canada, through the Ontario Genomics Institute (2007-OGI-TD-05).

Subscribe to genemania-announce