Extended Data Fig. 4: Tissue specificity of QTLs.
(a) Tissue sharing profile of mQTLs and eQTLs. (b-c) Cross-tissue sharing of mCpGs and eGenes. Cross-tissue mean percent of mCpGs and eGenes per tissue-sharing category is shown in parentheses. Of note, testis is an outlier for eQTL tissue specificity, as 23.5% of eGenes were not detected in any other tissue. Avg.: average (mean). (c) Cross-tissue sharing of mQTL tissue-leveraged effect magnitudes (y axis) per gene regulatory region (x axis, 36 data points per box plot). P-values of paired two-sided Wilcoxon signed rank tests are shown for corresponding pairwise comparisons; p-value of Kruskal-Wallis rank sum test is shown for the three-way comparison. Enh.: Enhancer. (d, e) Validation of tissue-specific mQTLs in muscle, blood and brain mQTL external cohorts, see (b) for tissue color legend. In (d), for each cohort, the average of absolute mQTL effect sizes and corresponding standard error is displayed for each set of tissue-specific mQTLs identified in each GTEx tissue (x axis). In (e), Spearman correlation between external and GTEx mQTL effect sizes, and associated standard error, is shown. Fisher’s z transformation was applied to Spearman correlation coefficients; standard errors were calculated based on the transformed coefficients. In (d,e), the number of QTL associations (N) tested for each pairwise comparison is as follows: NFUSION,GTEx = 195|4142|336,4630,287,4643|1428|360|369, NGoDMC,GTEx = 22|1353|47|1478|70|1019|292|83|102 and NROSMAP,GTEx = 57|2428|156|2587|163|2673|791|214|109, where GTEx corresponds to Breast|Colon|Kidney|Lung|Muscle|Ovary|Prostate|Testis|Blood tissues, respectively.
