GeneMANIA Prediction Server 2013 Update

By K. Zuberi, Max Franz, Harold Rodriguez, J. Montojo, C. Lopes, Gary D. Bader, Quaid D. Morris. 2013

398 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

Predicting multicellular function through multi-layer tissue networks (2017, methodology): “Notice that we exclude GeneMania in the comparison because it is not amenable to transfer learning.”
The BioGRID interaction database: 2015 update (2014, background): “…also accessible to the individual researcher indirectly through a number of other biological databases including NCBI Entrez-Gene (48), Uniprot (49), DroID (80), GermOnline (81), FlyBase (42), TAIR (73), SGD (41), PomBase (43), STRING (47), iRefIndex (82), GeneMania (83) and Pathway Commons (50).”
Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects (2016, positive): “EcoRI digested samples (10 ng of genomic DNA) were analyzed in triplicate by ddPCR using the Fam-labeled CNV probe and HEX-labeled reference probe M0005 RPP30-HEX (Supplementary Synaptic and ARC-complex genes intersected by a rare loss in at least 4 case or control subjects and with genic burden Ben”
STRING v10: protein–protein interaction networks, integrated over the tree of life (2014, methodology): “These include STRING, as well as GeneMANIA (21), FunCoup (18), I2D (22), ConsensusPathDB (22) and others.”
GeneMANIA update 2018 (2018, background): “There have been two previous publications describing the server, its features and its prediction accuracy (1,2).”