MAGENTA protocols

MAGENTA specifications

Information


Unique identifier OMICS_00236
Name MAGENTA
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 IN pipelines

 (2)
2018
PMCID: 5772158
PMID: 29282330
DOI: 10.1212/WNL.0000000000004820

[…] available variant function predicting software annovar.20 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 […]

2013
PMCID: 3772043
PMID: 24068947
DOI: 10.1371/journal.pgen.1003751

[…] total, 2,095,209 snps that were either directly genotyped or imputed and overlapped in all three studies and passed quality control were tested for association., we performed pathway analysis using meta-analysis gene-set enrichment of variant associations (magenta) [48]. magenta first maps snps to genes (defined as from 20 kb upstream of the 5′ utr to 10 kb downstream), and then selects […]

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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