Identification of transcriptomic features in regions or disease conditions may be confounded by changes in cell-type composition. We used PSEA24 to examine the impact of this confounding factor and found that all 960 BRGs remained differentially expressed between regions R1 and R6 in the AHBA. We also applied PSEA in the two PD datasets that allowed us to examine cell-type specificity between regions as well as between disease conditions. Although it is known that gene expression varies more between regions than between disease conditions22, it is less clear how cell-type composition contributes to this variation. Here, we found that regional comparisons yielded more significant results than when comparing disease conditions. Therefore, BRGs also captured expression changes between patients and controls, but changes were less dependent on cell-type abundance between regions than between patients and controls.
