Extended Data Fig. 8: Tissue-sharing properties of eQTL.
From: Genetic regulation of gene expression across multiple tissues in chickens
Absolute effect size (allelic fold change, aFC) of eQTLs (a), distance of eQTL to TSS (b), and minor allele frequency (c) as a function of the number of tissues in which the eGene is expressed. The black line represents the median estimate, and the grey shading indicates interquartile ranges. P values were computed via the asymptotic t-approximation. (d) Fraction of eQTLs around transcription start site (TSS) based on the number of tissues in which they are active in. (e) Fold enrichment (log2 scaled, mean ± s.d., y-axis) of tissue-specific and -shared eQTLs across 15 chromatin states. Error bars indicates standard errors of enrichment, with E1–E15 representing chromatin states defined previously14. (f) Manhattan plot for eQTL mapping of ALG3 in the liver, muscle, brain, and blood. The color legend represents the degree of linkage disequilibrium (LD, r2) between the top SNP and the rest. (g) and (h) Comparison of blood-specific eQTLs (Specific, n = 11,884) and the rest of blood eQTLs (Common, n = 9,089) in terms of Minor Allele Frequency (MAF) and effect size, respectively. Statistical significance was determined using a two-tailed Student’s t-test. (i) Opposite effects of lead variants on FBXO5 and ELAC2 in different tissues. Top panel: The effect of lead variant rs315639985 on FBXO5 in blood is opposite to that of rs312482960 in spleen. These two SNPs are in high LD (r2 = 0.92 in blood, r2 = 0.83 in spleen). Bottom panel: The effect of lead variant rs313608694 on ELAC2 in embryo is opposite to that in spleen. (j) Replication (π1) of eQTLs in liver across different breeds: Ross (n = 101), Leghorn (n = 74), Cobb (n = 47), and RIR (Rhode Island Red, n = 78). (k) Heatmap depicting eQTL effect sharing between breeds. (l) Expression of ENSGALG00000028174 (PRKCDBP) regulated by rs314795649 genotypes, consistent across all four breeds (n = 286 samples). Boxplot details: The central band represents the median, the box boundaries represent the 25% to 75% percentiles, and the whiskers extend 1.5 × the interquartile range.
