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MAGMA GTEx

I applied MAGMA1 to the lupus GWAS of Bentham et al.2 using bulk RNAseq data from GTEx3 as a reference. The gene-property analysis results are plotted below.

Result of MAGMA GTEx applied to Bentham et al.'s lupus GWAS. The x axis corresponds to tissue type, while the y axis measures MAGMA significance level.

The tissue types small intestine lymphode aggregate, spleen, EBV-transformed_lymphocytes, and whole blood are immunological, as befits lupus, an immune-mediated disease. The relevance of other tissue types, which are gut-related, is less obvious

  1. Christiaan A De Leeuw, Joris M Mooij, Tom Heskes, and Danielle Posthuma. MAGMA: generalized gene-set analysis of GWAS data. PLoS Computational Biology, 11(4):e1004219, 2015. URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004219. ↩

  2. James Bentham, David L Morris, Deborah S Cunninghame Graham, Christopher L Pinder, Philip Tombleson, Timothy W Behrens, Javier Martín, Benjamin P Fairfax, Julian C Knight, Lingyan Chen, and others. Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nature Genetics, 47(12):1457–1464, 2015. URL: https://pmc.ncbi.nlm.nih.gov/articles/PMC4668589/. ↩

  3. GTEx Consortium. The GTEx consortium atlas of genetic regulatory effects across human tissues. Science, 369(6509):1318–1330, 2020. URL: https://www.science.org/doi/full/10.1126/science.aaz1776. ↩