Interestingly, when partitioning the full sample-level matrix into correlations between samples from different tissues of the same individual, the same tissue across individuals, or different individuals and different tissues (Fig. 3C), we found more complex relationships between total expression and allelic ratios. As expected, expression levels are determined by tissue, and samples cluster by tissue (75.6% of variance; Fig. 3E and table S8B). However, allelic ratios show the opposite pattern (Fig. 3D), with higher correlation among tissues within the same individual (17.9% of variance) than among individuals for the same tissue (8.6%). These results indicate that ASE is primarily determined by the common genome among different tissues of the same individual (34). This suggests that the two dimensions of gene expression variability, gene expression levels and allelic ratios, are largely defined by independent factors.
