Because related tissues have highly overlapping gene sets and we fit each tissue without adjusting for the other tissues, related tissues often appear enriched as a group. In this analysis and the analysis in the next section, both focused on identifying system-level enrichments, these correlated results do not limit interpretability. In later sections, we focus on differentiating among related tissues/cell types within a system. We note also that the correlation structure among annotations can lead to a distribution of P values that is highly non-uniform (Online Methods).
