To compare between-sample and between-tissue sharing of ASE with the overall similarity of gene expression, we constructed two Spearman rank correlation matrices between all pairs of samples. In one, we correlated ASE ratios, capturing sharing of cis regulation; in the other, we correlated total coverage of the same sites, capturing similarity of overall gene expression levels, analyzing genes that are expressed in both tissues (both matrices used counts of reads covering heterozygous sites shared between the compared pair of samples) (14). The two matrices of tissue medians were highly correlated (Mantel test, r = 0.772, P < 0.0001; fig. S19), indicating that tissues with similar gene expression profiles also have a higher degree of sharing of genetic regulatory effects.
