The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

By David Warde-Farley, S. Donaldson, Ovi Comes, K. Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, C. Lopes and 7 more. Nucleic Acids Res., 2010

4,421 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 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. Six organisms are currently supported (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Homo sapiens and Saccharomyces cerevisiae) and hundreds of data sets have been collected from GEO, BioGRID, Pathway Commons and I2D, as well as organism-specific functional genomics data sets. Users can select arbitrary subsets of the data sets associated with an organism to perform their analyses and can upload their own data sets to analyze. The GeneMANIA algorithm performs as well or better than other gene function prediction methods on yeast and mouse benchmarks. The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make GeneMANIA a useful tool for any biologist.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d7f012f3290fb4a19a4ad91557f4ae02ed65a139

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Citations in the corpus

The BioGRID interaction database: 2017 update (2016, background): “This feature enables external resources such as NCBI (29), Uniprot (28) and others (23– 25, 27, 30, 31 , 39 , 74– 76”
Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR (2015, background): “Selected genes can be visualized in terms of their interaction network and function via GeneMANIA [27].”
FMRP Modulates Neural Differentiation through m6A-Dependent mRNA Nuclear Export (2019, positive): “The gene interaction network schematic was generated using GENEmania (Warde-Farley et al., 2010).”
Paradoxical effects of obesity on T cell function during tumor progression and PD-1 checkpoint blockade (2018, neutral): “This TMA was stained using validated / standardized multiplexed QIF panels as previously described 54 .”
STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012, background): “These include GeneMANIA (23), Consensus-PathDB (24), I2D (25), VisANT (26) and, more recently, hPRINT (27), HitPredict (28), IMID (29) and IMP (30).”
GeneMANIA update 2018 (2018, background): “There have been two previous publications describing the server, its features and its prediction accuracy (1,2).”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, background): “It is by no means the only such site: related resources that are currently being actively maintained include VisANT (33), GeneMANIA (34), N-Browse (35), I 2 D (36), APID (37), bioPIXIE (38) and ConsensusPathDB (39).”
The BioGRID Interaction Database: 2011 update (2010, methodology): “BioGRID interaction data can also be accessed automatically through biological network visualization applications that include Osprey (26), Cytoscape (27), GeneMania (28) and ProHits (29).”
GeneMANIA Prediction Server 2013 Update (2013, methodology): “Assigned based on query weights Unregularized (5) GM-2008 (1) Gene Ontology-based weighting: BP, MF & CC SW (5)”