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Abstract
GeneMANIA (http://www.genemania.org) is a flexible user-friendly web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query gene list, GeneMANIA extends the list with functionally similar genes that it identifies using available genomics and proteomics data. GeneMANIA also reports weights that indicate the predictive value of each selected data set for the query. GeneMANIA can also be used in a function prediction setting: given a query gene, GeneMANIA finds a small set of genes that are most likely to share function with that gene based on their interactions with it. Enriched Gene Ontology categories among this set can sometimes point to the function of the gene. Seven organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens, Rattus norvegicus and Saccharomyces cerevisiae), and hundreds of data sets have been collected from GEO, BioGRID, IRefIndex and I2D, as well as organism-specific functional genomics data sets. Users can customize their search by selecting specific data sets to query and by uploading their own data sets to analyze.
Highlights
The GeneMANIA prediction server has been in operation for the past 3 years [1] 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 [2,3,4] and the algorithm used to assign weights to networks [2,5]
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by the GeneMANIA Cytoscape app [6], which makes similar functionality available for desktop use in addition to a set of unpublished software tools for power users that can be run from the command line that are described at http://pages.genemania.org/ tools/
Summary
The GeneMANIA prediction server (http://www. genemania.org) has been in operation for the past 3 years [1] 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 [2,3,4] and the algorithm used to assign weights to networks [2,5] (see Table 1 for details).
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