Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA)
A computational tool applied to genome-wide association variant summary statistics for a given complex disease or trait, that tests for enrichment of genetic associations amongst genes in biological pathways or other type of functional modules (Segrè et al., PLoS Genetics 2010).
eQTLEnrich, tests for enrichment of (modest to genome-wide significant) common variant associations amongst a set of eQTLs in a given tissue. Software package can be downloaded here (version on github coming soon): https://bit.ly/2Klcgvf
eGeneEnrich, tests whether target genes of eQTLs with top ranked GWAS p-values (e.g., p<0.05) are enriched in specific biological pathways or other types of gene sets. Software package can be downloaded here (version on github coming soon): https://bit.ly/2yVlskm
eQTLEnrich and eGeneEnrich were used in Gamazon ER*,†, Segrè AV*,†, van de Bunt M*, et al., Using an atlas of gene regulation across 44 human tissues to illuminate complex disease- and trait-associated variation, Nature Genetics, online publication June 28, 2018: https://www.nature.com/articles/s41588-018-0154-4.
A new version of QTLEnrich v2 is available on Github: https://github.com/segrelabgenomics/QTLEnrich. The confounder and null variant tables needed to run QTLEnrich v2 on GTEx v8 eQTLs and sQTLs can be downloaded here.
QTLEnrich v2 was applied in the GTEx v8 main paper: GTEx consortium, BioRxiv 2019 (provisionally accepted at Science 2020) to 87 GWAS of complex diseases and traits and eQTLs and sQTLs in 49 tissues. A methods paper is under preparation.