GeneMANIA protocols

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GeneMANIA computational protocol

GeneMANIA specifications

Information


Unique identifier OMICS_02695
Name GeneMANIA
Interface Web user interface
Restrictions to use None
Input data Some genes.
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio

Subtool


  • Network Assessor

Documentation


Maintainers


  • person_outline Quaid Morris <>
  • person_outline Gary Bader <>
  • person_outline Mohan Babu <>
  • person_outline GeneMANIA Team <>

Additional information


Desktop: http://apps.cytoscape.org/apps/genemania http://pages.genemania.org/help/

Information


Unique identifier OMICS_02695
Name GeneMANIA
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Javascript, Python, Shell (Bash)
Computer skills Medium
Version 3.5.0
Stability Stable
Requirements
Cytoscape
Maintained Yes

Taxon


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio

Subtool


  • Network Assessor

Download


Versioning


Add your version

Documentation


Maintainers


  • person_outline Quaid Morris <>
  • person_outline Gary Bader <>
  • person_outline Mohan Babu <>
  • person_outline GeneMANIA Team <>

Additional information


Desktop: http://apps.cytoscape.org/apps/genemania http://pages.genemania.org/help/

Publications for GeneMANIA

library_books

GeneMANIA update 2018

2018 Nucleic Acids Res
PMCID: 6030815
PMID: 29912392
DOI: 10.1093/nar/gky311

GeneMANIA IN pipelines

 (10)
2018
PMCID: 5785814
PMID: 29370772
DOI: 10.1186/s12864-018-4444-0

[…] obtained were annotated against the chicken gene database from ensembl (release 84). all genes from regions under selection (top 1%) were further analyzed to predict the function of these genes with genemania prediction server [20] considering human database (chicken not available). gene enrichment analysis was performed considering q-values calculated from a fdr test, and pathways with q-values […]

2018
PMCID: 5807760
PMID: 29426343
DOI: 10.1186/s12989-018-0244-6

[…] 0.05, the go annotation or kegg pathway were considered significant. for gene functional classification analysis highest stringency was used and top five cluster was selected for interpretation. genemania web-tool was used for functional network analysis (http://www.genemania.org) [68]., primer sequences were designed according to online bioinformatics tool, primer bank […]

2018
PMCID: 5807760
PMID: 29426343
DOI: 10.1186/s12989-018-0244-6

[…] for gene functional classification analysis highest stringency was used and top five cluster was selected for interpretation. genemania web-tool was used for functional network analysis (http://www.genemania.org) [68]., primer sequences were designed according to online bioinformatics tool, primer bank (https://pga.mgh.harvard.edu/primerbank/index.html) [69–71]. the primers […]

2018
PMCID: 5832109
PMID: 29636777
DOI: 10.1155/2018/4509892

[…] with the keyword “cancer/tumor,” allowing elimination of protein targets that were irrelevant to cancer. the remaining proteins were considered as candidate targets in subsequent analyses., the genemania server can generate hypotheses about gene function, analyze gene lists, and prioritize genes for functional assays [14]. after selection of homo sapiens as the organism, interesting genes […]

2017
PMCID: 5415337
PMID: 28508063
DOI: 10.1126/sciadv.1602505

[…] the physical protein interaction databases corum and biogrid (biological general repository for interaction datasets) and a genetic interaction database to generate gene subnetworks using the genemania application from within cytoscape., five-week-old scid mice were purchased from charles river laboratories. three to 5 days of acclimatization after arrival, the inoculation area was shaved […]

GeneMANIA institution(s)
Department of Biochemistry, University of Regina, Regina, SK, Canada; Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Regina, Regina, SK, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada
GeneMANIA funding source(s)
Supported by grants from Global Leadership Round in Genomics and Life Sciences, by National Resource for Network Biology (P41 GM103504), Canadian Institutes of Health Research (CIHR), (MOP-130374), (MOP-82852), the National Sciences and Engineering Research Council of Canada, (DG-20234), a CIHR New Investigator award, a CIHR Vanier Graduate Scholarship and a Saskatchewan Postdoctoral Research Fellowship.

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