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. 2018 Jul 2;46(W1):W60-W64.
doi: 10.1093/nar/gky311.

GeneMANIA update 2018

Max Franz  1 , Harold Rodriguez  1 , Christian Lopes  1 , Khalid Zuberi  1 , Jason Montojo  1 , Gary D Bader  1   2   3 , Quaid Morris  1   2   3   4
Affiliations

GeneMANIA update 2018

Max Franz et al. Nucleic Acids Res. .

Abstract

GeneMANIA (http://genemania VSports手机版. 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. .

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Figures

Figure 1.
Figure 1.
The initial GeneMANIA query view (top) and the result view (bottom). The new query history feature is shown at the bottom of query view.
Figure 2.
Figure 2.
Layouts supported by GeneMANIA, from left to right: concentric bipartite, force-directed, linear bipartite.
See this image and copyright information in PMC

References

    1. Warde-Farley D., Donaldson S.L., Comes O., Zuberi K., Badrawi R., Chao P., Franz M., Grouios C., Kazi F., Lopes C.T. 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. Zuberi K., Franz M., Rodriguez H., Montojo J., Lopes C.T., Bader G.D., Morris Q.. GeneMANIA prediction server 2013 update. Nucleic Acids Res. 2013; 41:W115–W122. - PMC (V体育安卓版) - 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:S4. - PMC - PubMed
    1. Mostafavi S., Goldenberg A., Morris Q.. Predicting node characteristics from molecular networks. Network Biol.: Methods Applic. 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 (VSports app下载)

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