The GeneMANIA prediction server (http://www.genemania.org) has been in operation for the past 3 years (1) although prototypes with limited functionality were available from 2008 (2). Details about the server and its prediction accuracy on benchmark data sets are available in the original NAR Web server article (1) and associated publications that describe the label propagation algorithm used by GeneMANIA to find related genes (2–4) and the algorithm used to assign weights to networks (2,5) (see Table 1 for details). The prediction server is complemented by the GeneMANIA Cytoscape app (6), which makes similar functionality available for desktop use in addition to a set of unpublished software tools for power users that can be run from the command line that are described at http://pages.genemania.org/tools/. See Table 2 for a list of additional resources associated with GeneMANIA. Table 1.GeneMANIA network weighting algorithmsName in ‘advanced options panel’Validation: Algorithm name (citation)Assigned based on query weightsUnregularized (5)GM-2008 (1)Gene Ontology-based weighting: BP, MF & CCSW (5)Equal weighting: equal by networkUniform (5) Table 2.GeneMANIA associated resourcesResourceLocationDescriptionGeneMANIA Cytoscape appCytoscape app storeDesktop app with all GeneMANIA functionality as well
