Extended Data Fig. 3: Tissue specificity of m6A-QTL.
From: Genetic drivers of m6A methylation in human brain, lung, heart and muscle
a. Summary of shared/specific g-m6As and m6A across tissues. b. KEGG pathway enrichments for tissue-specific gmGenes. c. Tissue-intersections of the eQTLs identified from the same samples for m6A-QTL calling. d,e. Correlation between p-value (x-axis) and eQTL effect (y-axis) between tissues, with positive- and negative-effect eQTLs separated for full GTEx-V8 (d)), and subsampled to individuals used here (e;). f. Nominal p-values (y-axis) of simulated m6A-QTLs (Positive), and simulated NULL m6A-QTLs controls without QTL effects (Control). Boxes=25%–75% percentile; line=median; whiskers=1.5 IQR. g. m6A-QTL overlaps between tissues in simulated data show much higher tissue-sharing (teal curve) than in observed real data (peach curve). h. Effect sizes directionality between m6A-QTL from real tissue data and simulated data are almost 100% consistent. i. Effect directionality consistency when m6A-QTLs were identified with 50, 38 and 30 samples. j. Gene expression distribution of the tissue-specific vs. tissue-shared m6A-QTLs in each tissue. k. Gene expression in tissues for tissue-specific gmGenes in each tissue. Statistical test was carried out by two-sided paired Wilcoxon test. l. Correlation (adjusted R2) of eQTLs between GTEx primary tissues and YRI LCL cells. Boxes=25%–75% percentile; line=median; whiskers=1.5 IQR. m. Comparison of m6A-QTL effects size between this study (eGTEx tissues, x-axis) and the other m6A-QTL study (YRI LCLs, y-axis). Green dots represent the m6A-QTLs shared by the two studies. Directionality consistency and corresponding p-value (vs. the 50% expected by chance) calculated using one-sided Fisher exact test (inset box). n. Correlation of m6A-QTLs between eGTEx primary tissues and YRI LCLs. o. Correlation between p-value and m6A-QTL effect in LCL cell lines for m6A-QTLs identified in eGTEx tissues, with positive- and negative-effect eGTEx m6A-QTLs separated. Directionality consistency and corresponding p-value (vs. the 50% expected by chance) calculated using one-sided Fisher exact test.
