Many features of the brain transcriptome are apparent with this visualization. Remarkably few differences are seen at this fold change threshold across the neocortex (Fig. 4a, upper left) and cerebellum (lower right), reflecting their stereotyped repetitive cytoarchitecture. Exceptions to this relative cortical homogeneity include the postcentral gyrus (primary sensory cortex), temporal pole (area 38) and primary visual cortex (area 17). In contrast, complex differential relationships were observed between specific nuclei in subcortical structures. The globus pallidus and striatum have highly distinct profiles, as do several specific subcortical regions including the midbrain raphe, pontine nuclei and inferior olivary complex. The magnitude of differential expression between pairs of structures is also strongly correlated with the number of differentially expressed genes between these structures (Pearson r = 0.62, P < 10−16; Supplementary Fig. 4).
