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. 2013 Jul;41(Web Server issue):W115-22.
doi: 10.1093/nar/gkt533.

GeneMANIA prediction server 2013 update

Khalid Zuberi  1 , Max Franz, Harold Rodriguez, Jason Montojo, Christian Tannus Lopes, Gary D Bader, Quaid Morris
Affiliations

GeneMANIA prediction server 2013 update

Khalid Zuberi et al. Nucleic Acids Res. 2013 Jul.

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.

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Figures

Figure 1.
Figure 1.
Screenshot of default search for related genes to GRN. Functions tab of the results screen is selected and top two most enriched functions are colored.
Figure 2.
Figure 2.
Close-up of attribute node in GeneMANIA results window. Shows attribute node for InterPro domain ‘DNA_recomb/repair_Rad51_C’ linked to genes in the results window that contain that attribute.
See this image and copyright information in PMC

References

    1. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 2010;38:W214–W220. - PMC - PubMed
    1. Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol. 2008;9(Suppl. 1):S4. - PMC - PubMed
    1. Mostafavi S, Goldenberg A, Morris Q. Predicting node characteristics from molecular networks. Methods Mol. Biol. 2011;781:399–414. - PubMed
    1. Mostafavi S, Morris Q. Combining many interaction networks to predict gene function and analyze gene lists. Proteomics. 2012;12:1687–1696. - PubMed
    1. Mostafavi S, Morris Q. Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinformatics. 2010;26:1759–1765. - PMC - PubMed

Publication types