GeneMANIA statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool GeneMANIA
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Tool usage distribution map

This map represents all the scientific publications referring to GeneMANIA per scientific context
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Associated diseases

This word cloud represents GeneMANIA usage per disease context
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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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Protocols

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


download.png
github.png

Versioning


No version available

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 citations

 (385)
library_books

Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes

2018
PMCID: 5943605
PMID: 29743561
DOI: 10.1038/s41419-018-0600-3

[…] ot3d.ggplot2 http://ggplot2.tidyverse.org/.Pheatmap https://cloud.r-project.org/web/packages/pheatmap/.Cytoscape http://www.cytoscape.org/.EnrichmentMap http://www.baderlab.org/Software/EnrichmentMap.GeneMANIA https://www.genemania.org/.ENCODE https://www.encodeproject.org/. […]

call_split

Genetic variants of ALDH2 rs671 and CYP2E1 rs2031920 contributed to risk of hepatocellular carcinoma susceptibility in a Chinese population

2018
PMCID: 5942392
PMID: 29765251
DOI: 10.2147/CMAR.S162105
call_split See protocol

[…] evels 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 inte […]

call_split

Genome wide association pathway analysis to identify candidate single nucleotide polymorphisms and molecular pathways associated with TP53 expression status in HBV related hepatocellular carcinoma

2018
PMCID: 5937480
PMID: 29760565
DOI: 10.2147/CMAR.S163209
call_split See protocol

[…] d 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 w […]

library_books

Development of a computational promoter with highly efficient expression in tumors

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

[…] that 9 TFs were well studied and published in more than 100 articles. The top 3 selected TFs were HIF-1α, CREB and NF-κB.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 that they are involved […]

library_books

Whole exome sequencing reveals rare variants linked to congenital pouch colon

2018
Sci Rep
PMCID: 5923232
PMID: 29703930
DOI: 10.1038/s41598-018-24967-y

[…] quencing (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 contr […]

library_books

Circulating miRNAs as Putative Biomarkers of Exercise Adaptation in Endurance Horses

2018
Front Physiol
PMCID: 5928201
PMID: 29740341
DOI: 10.3389/fphys.2018.00429

[…] (PPI) network and the PSIQUIC service (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/home.xhtml) was used to download proteins interactions from six different public databases (ChEMBL, Spike, GeneMania, mentha, MINT, IntAct). These six networks were merged together in order to generate a unique PPI network with all the interactions. Only Homo sapiens interactions were used to build the new […]


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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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