GeneMANIA prediction server 2013 update.
paper
Cited
Public
- Authors
- Zuberi, Khalid; Franz, Max; Rodriguez, Harold; Montojo, Jason; Lopes, Christian Tannus; Bader, Gary D; Morris, Quaid
- Year
- 2013
- Journal
- Nucleic acids research
- PMID
- 23794635
- DOI
- 10.1093/nar/gkt533
- PMCID
- PMC3692113
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.
Screenshot of default search for related genes to GRN. Functions tab of the results screen is selected and top two most enriched functions are colored.
Close-up of attribute node in GeneMANIA results window. Shows attribute node for InterPro domain βDNA_recomb/repair_Rad51_Cβ linked to genes in the results window that contain that attribute.
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| Name | Type |
|---|---|
| Cytoscape local | drug |
| @genemania local | drug |
| GeneMANIA local | drug |
| genemania-announce local | drug |
| GeneMANIA bulk data download local | drug |
| GeneMANIA co-expression network local | cohort |
| GeneMANIA command line tools local | drug |
| GeneMANIA Cytoscape app local | drug |
| GeneMANIA data reports local | drug |
| GeneMANIA Desktop app local | drug |
| GRN local | gene |
| GSE series local | cohort |
| lysosomal lumen local | drug |
| lysosome | drug |
| query genes local | gene |
| related genes local | gene |
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| KAT2B polymorphism identified for drug abuse in African Americans with regulatory links to drug abuse pathways in human prefrontal cortex. | Johnson EO et al. | β | 2016 | β |
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| Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. | Oughtred R et al. | β | 2016 | β |
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| Constructing simple biological networks for understanding complex high-throughput data in plants. | Moyano TC et al. | β | 2015 | β |
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| Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates. | Boloc D et al. | β | 2015 | β |
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| Suppression of ASKΞ² (AtSK32), a Clade III Arabidopsis GSK3, Leads to the Pollen Defect during Late Pollen Development. | Dong X et al. | β | 2015 | β |
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