For gene expression, RCA revealed that the brain separates from the other tissues in the first component (Fig. 3E and fig. S26). In particular, for the brain, intertissue comparisons exhibit more differences than intratissue ones (figs. S27 to S30). A different picture emerged for chromatin. The H3K27ac chromatin levels at all regulatory positions were, overall, less distinguishable between the brain and other tissues (Fig. 3C) (21). At first glance, this is surprising, as one expects great differences in enhancer usage between tissues. However, our analysis compares chromatin signals over all regulatory elements from ENCODE (including enhancers and promoters), which is logically consistent with our expression comparison across all protein-coding genes (Fig. 3, F versus C, and tables S5 to S7). As the total number of human regulatory elements is much larger than the number of brain-active enhancers (~1.3 million versus ~79,000), our results likely reflect the fact that there are proportionately fewer brain-active regulatory elements than protein-coding genes (6% versus 60%).
