Comparison of CTX and CTX_95 revealed that a majority of gene coexpression modules were present in both cortical networks. A majority of gene coexpression modules identified in CTX were also present in CTX_ILMN. The notable similarity among these networks, constructed from different cortical areas, individuals and microarray platforms, suggests a fundamental organization to the transcriptome of human cerebral cortex that has not previously been recognized. Modules enriched with markers of major cell classes were identified in cerebral cortex, caudate nucleus and cerebellum. The consistent identification of these modules across brain regions suggests that they constitute molecular correlates to the cellular building blocks of the nervous system. Other modules identified in this analysis distinguished additional cell types, including PVALB-positive interneurons, Purkinje neurons and meningeal cells, whereas still others related to mitochondrial, ribosomal and synaptic function, response to hypoxia, gender differences, and the subventricular neurogenic niche. For some modules, the importance of gene coexpression relationships will require further investigation. For example, our results suggest that coexpression in M13A may relate to the migration and assimilation of immature interneurons in adult cerebral cortex.
