Fig. 5: Significant results in GWAS across 189 infiltration phenotypes.
The Venn diagrams in a and b display the number of infiltration phenotypes with a significant variant identified within each analysis procedure. a Empirical Brown’s Method: P < 5 × 10−8. xCell, Cibersort-Relative, and Cibersort-Absolute: P < 10−5. b All P < 5 × 10-8. Figures c–h relate to the two most significant genetic associations. In all, 5+ million genome-wide genetic variants were tested for association with Helper T cells in thyroid samples (top row) and lymphocytes in sigmoid colon samples (bottom row). The SNP-association Empirical Brown’s p-values are visualized along the y-axis in a qq-plot (leftmost column), where the x-axis represents the expected –log10 p-values under the null distribution. The association between the most significant variant from the GWAS and the phenotype (using the transformed residuals) is visualized in the middle column. The right column displays the association between the phenotype (transformed raw scores) and tissue gene expression of variant-associated eGenes, with expression values split into three groups in the 33rd and 67th percentile of expression. For visualization purposes, CIBERSORT-Absolute scores are displayed in the middle and right columns. In d, e and g, h, data are summarized as boxplots where the middle line is the median, the lower and upper hinges represent the first and third quartiles, and the whiskers extend from the hinge with a length of 1.5x the inter-quartile range. All data points are plot individually. Due to non-present genetic data for some donors between v6 and v7 releases, n = 281 samples are used in d and n = 446 samples are used in e. Similarly, n = 121 samples are used in g and n = 233 samples are used in h. Figure i describes the statistical test results for whether there is an enrichment of eQTLs in the iQTL genetic results for each infiltration phenotype, where infiltration phenotypes are sorted along the x-axis by the enrichment test’s –log10 p-values. Source data for a, b, e–i are provided as a Source Data file.
