Home LiteratureArticle Details
PMID: 23794635 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

GeneMANIA prediction server 2013 update.

Nucleic acids research ·Vol. 41 ·No. Web Server issue ·2013-07-00 ·Pages W115-22

Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q

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.

MeSH Terms
Algorithms Animals Gene Regulatory Networks Genes Humans Internet Mice Rats Software
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Zuberi Khalid
The Donnelly Centre, University of Toronto, Ontario, Canada.
Franz Max
Rodriguez Harold
Montojo Jason
Lopes Christian Tannus
Bader Gary D
Morris Quaid
References (35)
35 references, click to expand
  1. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.
    Genome Biol. 2009;10(11):R130 PMID: 19919682
  2. Molecular signatures database (MSigDB) 3.0.
    Bioinformatics. 2011 Jun 15;27(12):1739-40 PMID: 21546393
  3. Fast integration of heterogeneous data sources for predicting gene function with limited annotation.
    Bioinformatics. 2010 Jul 15;26(14):1759-65 PMID: 20507895
  4. Model-based gene set analysis for Bioconductor.
    Bioinformatics. 2011 Jul 1;27(13):1882-3 PMID: 21561920
  5. iRefIndex: a consolidated protein interaction database with provenance.
    BMC Bioinformatics. 2008 Sep 30;9:405 PMID: 18823568
  6. MINT, the molecular interaction database: 2012 update.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D857-61 PMID: 22096227
  7. RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network.
    Genome Biol. 2012 Dec 26;13(12):R125 PMID: 23268829
  8. A human functional protein interaction network and its application to cancer data analysis.
    Genome Biol. 2010;11(5):R53 PMID: 20482850
  9. InterPro in 2011: new developments in the family and domain prediction database.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12 PMID: 22096229
  10. The impact of multifunctional genes on "guilt by association" analysis.
    PLoS One. 2011 Feb 18;6(2):e17258 PMID: 21364756
  11. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.
    Genome Biol. 2008;9 Suppl 1:S2 PMID: 18613946
  12. Cytoscape Web: an interactive web-based network browser.
    Bioinformatics. 2010 Sep 15;26(18):2347-8 PMID: 20656902
  13. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
    Nucleic Acids Res. 2002 Jan 1;30(1):207-10 PMID: 11752295
  14. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
    Nat Protoc. 2009;4(1):44-57 PMID: 19131956
  15. PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
    Nat Methods. 2011 Jun 29;8(7):528-9 PMID: 21716279
  16. GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.
    Bioinformatics. 2010 Nov 15;26(22):2927-8 PMID: 20926419
  17. Comparative interactomics with Funcoup 2.0.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D821-8 PMID: 22110034
  18. The BioGRID interaction database: 2013 update.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D816-23 PMID: 23203989
  19. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.
    PLoS One. 2010 Nov 15;5(11):e13984 PMID: 21085593
  20. Predicting node characteristics from molecular networks.
    Methods Mol Biol. 2011;781:399-414 PMID: 21877293
  21. FuncBase: a resource for quantitative gene function annotation.
    Bioinformatics. 2010 Jul 15;26(14):1806-7 PMID: 20495000
  22. STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15 PMID: 23203871
  23. Saccharomyces Genome Database: the genomics resource of budding yeast.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5 PMID: 22110037
  24. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
    Nucleic Acids Res. 2010 Jul;38(Web Server issue):W214-20 PMID: 20576703
  25. Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function.
    Nucleic Acids Res. 2011 Nov 1;39(20):8677-88 PMID: 21785136
  26. Evaluation of linguistic features useful in extraction of interactions from PubMed; application to annotating known, high-throughput and predicted interactions in I2D.
    Bioinformatics. 2010 Jan 1;26(1):111-9 PMID: 19850753
  27. Prioritizing candidate disease genes by network-based boosting of genome-wide association data.
    Genome Res. 2011 Jul;21(7):1109-21 PMID: 21536720
  28. Combining many interaction networks to predict gene function and analyze gene lists.
    Proteomics. 2012 May;12(10):1687-96 PMID: 22589215
  29. Browsing multidimensional molecular networks with the generic network browser (N-Browse).
    Curr Protoc Bioinformatics. 2008 Sep;Chapter 9:Unit 9.11 PMID: 18819079
  30. BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species.
    Plant J. 2012 Sep;71(6):1038-50 PMID: 22607031
  31. WormBase 2012: more genomes, more data, new website.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D735-41 PMID: 22067452
  32. Labeling nodes using three degrees of propagation.
    PLoS One. 2012;7(12):e51947 PMID: 23284828
  33. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function.
    Genome Biol. 2008;9 Suppl 1:S4 PMID: 18613948
  34. Discovery of biological networks from diverse functional genomic data.
    Genome Biol. 2005;6(13):R114 PMID: 16420673
  35. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.
    Nucleic Acids Res. 2012 Jul;40(Web Server issue):W484-90 PMID: 22684505
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkt533
Published
2013-07-00
Pages
W115-22
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3692113
Subset
IM
Grants
NIGMS NIH HHS · P41 GM103504 · United States
External Links
PubMed source DOI: 10.1093/nar/gkt533 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2