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MAGMA GTEx

I applied MAGMA1 to Human Herpesvirus 7 DNA GWAS of Kamitaki 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 Kamitaki et al's HHV7 DNA GWAS. The x axis corresponds to tissue type, while the y axis measures MAGMA significance level.

Consistent with the role of the immune system of maintaining HHV7 in a dormant state, the top three tissue types in this analysis are Ileum Lymphode Aggregate, Whole Blood, and Spleen, all of which are immune-related. As noted by Finucate et al., lung tissue in the GTEx dataset also probably contains immune cells4, so it makes sense for lung tissue to be significant. The three other tissue types all gut-related. Their significant is less clear, but may reflect the role of intestinal tissue as an important site of HHV7 latency5.

Reproducing Analysis

To reproduce the above, run the HHV7 Analysis Script.

  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. Nolan Kamitaki, David Tang, Steven A McCarroll, and Po-Ru Loh. Genes and environment profoundly affect the human virome. bioRxiv, pages 2025–09, 2025. URL: https://www.biorxiv.org/content/10.1101/2025.09.08.674901. ↩

  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. ↩

  4. Hilary K Finucane, Yakir A Reshef, Verneri Anttila, Kamil Slowikowski, Alexander Gusev, Andrea Byrnes, Steven Gazal, Po-Ru Loh, Caleb Lareau, Noam Shoresh, and others. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nature Genetics, 50(4):621–629, 2018. URL: https://pmc.ncbi.nlm.nih.gov/articles/PMC5896795/. ↩

  5. Arianna Gonelli, Sergio Boccia, Michela Boni, Alessandro Pozzoli, Caterina Rizzo, Patrizia Querzoli, Enzo Cassai, and Dario Di Luca. Human herpesvirus 7 is latent in gastric mucosa. Journal of medical virology, 63(4):277–283, 2001. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/1096-9071(200104)63:4%3C277::AID-JMV1002%3E3.0.CO;2-K. ↩