To assess whether differences in CpG methylation and expression were consistently different between brain regions, our initial analyses focused on global comparison of these measures across tissues. Performing a hierarchical cluster analysis [9] of these data demonstrated that the four brain regions have different epigenetic and expression profiles (Figure 1A and 1B). Expression pattern differences were distinct between cerebellum, pons and cortical tissue, with frontal and temporal cortices clearly separating within the mRNA dataset, but overlapping within the CpG methylation data. These data show that CpG methylation and mRNA levels vary measurably between brain regions. These data are in agreement with previous work that demonstrated distinct patterns of gene expression and DNA methylation in human cerebellum compared to cortical tissues [10], [11].
