Abstract
GeneMANIA (http://genemania.org) is a flexible user-friendly web site for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Given a query gene list, GeneMANIA finds functionally similar genes using a wealth of genomics and proteomics data. In this mode, it weights each functional genomic dataset according to its predictive value for the query. Another use of GeneMANIA is gene function prediction. Given a single query gene, GeneMANIA finds genes likely to share function with it based on their interactions with it. Enriched Gene Ontology categories among this set can point to the function of the gene. Nine organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Escherichia coli, Homo sapiens, Mus musculus, Rattus norvegicus and Saccharomyces cerevisiae). Hundreds of data sets and hundreds of millions of interactions 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. We have recently updated the user interface to GeneMANIA to make it more intuitive and make more efficient use of visual space. GeneMANIA can now be used effectively on a variety of devices.
Highlights
The GeneMANIA prediction server has been in operation for seven years [1]
The prediction server functionality is mirrored by a Cytoscape app [7] for desktop use, and the function prediction algorithms are available as a set of software tools that can be run from the command line for large-scale automation
We describe updates to the GeneMANIA prediction server, Cytoscape app, and data sets that have occurred over the past five years
Summary
The GeneMANIA prediction server (http://genemania.org) has been in operation for seven years [1]. There have been two previous publications describing the server, its features and its prediction accuracy [1,2]. The prediction server functionality is mirrored by a Cytoscape app [7] for desktop use, and the function prediction algorithms are available as a set of software tools that can be run from the command line for large-scale automation. All of GeneMANIA’s data are available for download from our webserver (http://genemania.org/data) and via web services through our Cytoscape app [7]. We describe updates to the GeneMANIA prediction server, Cytoscape app, and data sets that have occurred over the past five years
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
