GeneMANIA statistics

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Citations per year

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Popular tool citations

chevron_left Gene set enrichment analysis Gene co-expression prediction Gene Ontology annotation chevron_right
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Associated diseases

Associated diseases

Protocols

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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

 (51)
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 [] 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) []., primer sequences were designed according to online bioinformatics tool, primer bank […]

2018
PMCID: 5818530
PMID: 29459627
DOI: 10.1038/s41598-018-21601-9

[…] gene ontology (go) enrichment analysis,. up-regulated and down-regulated genes in significant kegg pathways (p-value < 0.05) were used to generate protein–protein interaction networks using the genemania module in cytoscape on the basis of the mouse or human protein–protein interaction database., , myungsuk kim and jisun lim contributed equally to this work., a correction to this article […]

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 []. after selection of homo sapiens as the organism, interesting genes […]

2018
PMCID: 5924487
PMID: 29703163
DOI: 10.1186/s12885-018-4421-7

[…] to distinguish whether there was overlap in the two searches, and the number of references was calculated. articles published before 2016 were included in the present study., the ppi database genemania (http://genemania.org/) was used to obtain the interactions among the selected tfs, including nf-κb, creb and hif-1α. the proteins that interact with the selected tfs were predicted, […]


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GeneMANIA in publications

 (575)
PMCID: 5943605
PMID: 29743561
DOI: 10.1038/s41419-018-0600-3

[…] we then assessed whether ik6 expression conferred dominant-negative (dn) effects on ikzf1 in our models. the top 100 genes that showed possible physical interaction with ikzf1 were retrieved from genemania. unsupervised hierarchical clustering analysis of these genes in our rna-seq dataset revealed minimal differences between ik6 and ctrl samples (sfig. ). genes that are potentially regulated […]

PMCID: 5942392
PMID: 29765251
DOI: 10.2147/CMAR.S162105

[…] in different tissues and the merav website (http://merav.wi.mit.edu/; accessed july 1, 2017) was assessed to retrieve adlh2 and cyp2e1 expression levels in normal and primary tumor tissues. the genemania prediction server of biological network integration for gene prioritization and predicting gene function (http://genemania.org/; accessed july 1, 2017) was employed to explore potential […]

PMCID: 5937480
PMID: 29760565
DOI: 10.2147/CMAR.S163209

[…] the affymetrix ht human genome u133a array data set (thermo fisher scientific, waltham, ma, usa) of gse14520 in the co-expression analysis. gene multiple association network integration algorithm, (genemania; http://genemania.org, accessed february 20, 2017) and search tool for the retrieval of interacting genes/proteins, (string; http://string.embl.de/, accessed february 20, 2017) web servers […]

PMCID: 5924487
PMID: 29703163
DOI: 10.1186/s12885-018-4421-7

[…] were well studied and published in more than 100 articles. the top 3 selected tfs were hif-1α, creb and nf-κb.table 1, subsequently, the interactions involving these tfs were further analyzed using genemania. figure  shows the proteins that could interact with nf-κb, creb or hif-1α. using uniprot analysis, the functions of the gene products that interact with nf-κb suggest […]

PMCID: 5923232
PMID: 29703930
DOI: 10.1038/s41598-018-24967-y

[…] (wes) for a total of 64 samples including the unaffected siblings/parents, where available. the samples were analysed for mutations predicted to be causal. the datasets were filtered against genemania reference and checked for significant association of deleterious heterozygous germline mutations. while a marked impact on the risk of cpc specific genes in affected individuals versus […]


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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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