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MAGENTA specifications


Unique identifier OMICS_00236
Alternative name Meta-Analysis Gene-set Enrichment of variaNT Associations
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for Meta-Analysis Gene-set Enrichment of variaNT Associations

MAGENTA citations


Periodontal Infectogenomics

PMCID: 5937045
PMID: 29760828
DOI: 10.1186/s41232-018-0065-x

[…] ence of association for red and orange complex microbiota except Aggregatibacter actinomycetemcomitans []. These results are further carried forward in another genome association study using MAGENTA (meta-analysis gene set enrichment of variant associations) approach to obtain gene-centric and gene set association results. The statistically significant association has been found for 6 genes; 4 wit […]


A Meta Analysis of Genome Wide Association Studies of Growth Differentiation Factor 15 Concentration in Blood

Front Genet
PMCID: 5876753
PMID: 29628937
DOI: 10.3389/fgene.2018.00097

[…] -wide meta-analysis results from the discovery samples were tested for enrichment of genetic associations with pre-specified functionally related gene-sets and biological processes using the program, meta-analysis gene-set enrichment of variant associations (MAGENTA, Ver. 2.4, ). The MAGENTA analysis was run in a hypothesis-free way, and 6 public databases were combined and included in the analysi […]


Whole genome sequence analyses of brain imaging measures in the Framingham Study

PMCID: 5772158
PMID: 29282330
DOI: 10.1212/WNL.0000000000004820

[…] blicly available variant function predicting software Annovar. All association analyses were carried out using EPACTS 3.2.6 software (University of Michigan) with the EMMAX test. Finally, we used the Meta-Analysis Gene-set Enrichment of Variant Associations (MAGENTA) method to explore pathway-based associations using single-SNV association results. MAGENTA implements a gene set enrichment analysis […]


Genome wide association study of offspring birth weight in 86 577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics

Hum Mol Genet
PMCID: 5886200
PMID: 29309628
DOI: 10.1093/hmg/ddx429

[…] nfant head circumference () and primary or permanent tooth eruption (,).To identify biological pathways underlying maternal regulation of birth weight, we performed gene-set enrichment analysis using Meta-Analysis Gene-set EnrichmeNT of variant Associations (MAGENTA) (). Seven pathways reached false discovery rate (FDR) < 0.05, including three involved in the metabolism of xenobiotics (, Table S11 […]


Genome wide association and HLA region fine mapping studies identify susceptibility loci for multiple common infections

Nat Commun
PMCID: 5605711
PMID: 28928442
DOI: 10.1038/s41467-017-00257-5

[…] 4 (rs3862630, P = 1.21 × 10−8, OR = 1.13) also have highly significant associations with mumps. Both are components of the glycosphingolipid (GSL) biosynthesis pathway, which was the most significant Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA) -analyzed pathway (Table : P = 1 × 10−4 and false discovery rate (FDR) = 0.003) identified using mumps GWAS data. This pathway also […]


Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis

Nat Genet
PMCID: 5621629
PMID: 28869591
DOI: 10.1038/ng.3949

[…] ribed. The visualization of these ‘meta gene-sets’ was performed in cytoscape , filtering for ‘meta gene sets’ at FDR <1%.We also compared the DEPICT gene set enrichment results to analyses using the Meta-analysis gene-set enrichment of variant associations (MAGENTA) software. Briefly, MAGENTA maps each gene in the genome to a single index SNP with the lowest p value within a 110 kb upstream and 4 […]


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MAGENTA institution(s)
Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Clinical Sciences, Diabetes and Endocrinology Research Unit, University Hospital Malmö, Lund University, Malmö, Sweden; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Queensland Institute of Medical Research, QLD, Australia
MAGENTA funding source(s)
This project was supported by the American Diabetes Association (Award No.: 7-08-MN-OK), the Swedish Research Council (Linne grant), the Wallenberg Foundation, the Sigrid Juselius Foundation and the American Diabetes Association/Smith Family Foundation.

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