GeneMANIA update 2018

By Max Franz, Harold Rodriguez, C. Lopes, K. Zuberi, J. Montojo, Gary D. Bader, Quaid D. Morris. Nucleic Acids Res., 2018

1,209 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/143ede47629e84c7bf907400cf1639e1be3364c0

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In Molecular Biology

Citations in the corpus

The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest (2022, background): “Among frequently used and actively maintained frameworks are ConsensusPathDB (14), FunCoup (15), GeneMANIA (16), HumanBase (17), HumanNet (18), IID (19) and STRING (20–22).”
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets (2018, background): “The STRING database (‘Search Tool for Retrieval of Interacting Genes / Proteins’) belongs to this latter class, along with GeneMania (22), FunCoup (23), I2D (24), ConsensusPathDb (25), IMP (26) and HumanNet (27)––most of which have recently been reviewed and benchmarked in (7).”