The complete set of interaction networks used in the GeneMANIA system are now available for download at http://genemania.org/data/. The data is in plain text format and is described in detail on our data archive help page.
Included along with the interaction networks are additional files providing network source references as well as the gene identifiers used in the data processing. The individual files are simply tab-delimited text with a header row.
Current as well as previous data releases are available. You can identify datasets by their production date, this corresponds to the 'Last database update' field displayed at the top of the printable report that can be generated after running a query on the GeneMANIA website. The data download location organizes datasets into folders by this production date in year-month-day format, such as '2011-08-03'.
The data files are collected and compressed into a single large archive file per organism. As a guide to size, the files for the latest GeneMANIA data release total the following:
|Organism||# Networks||Archive size|
One additional and perhaps useful network is packaged separately, this is the combined network used by default when GeneMANIA performs queries on small gene lists. It's generated by integrating the individual default networks using a weighting method based on Biological Process Gene Ontology (GO) annotations. The network weights used to perform the integration are also provided in an additional file.
Note: the Cytoscape plugin uses a different format for networks and you should use its internal download system to retrieve data.
As always, feedback is welcome. The GeneMANIA contact form is available online.