Table 1.

A subset of over-represented functional groups and pathways known to play a role in neuronal plasticity (all over-represented groups are listed in supplemental Table 4, available at www.jneurosci.org as supplemental material). Six brain populations were examined: genes regulated in cortex (Whole Cortex) and cerebellum (Whole Cerebellum) and also enriched in four neuronal populations: cortical glutamate neurons (Glutamate enriched), cortical GABA neurons (GABA enriched), cerebellar Purkinje neurons (Purkinje enriched), and cerebellar granule neurons (Granule enriched). Color indicates a significance level from the over-representation analysis. Empty cells indicate the absence of over-represented groups from a particular functional domain in a particular brain population. The over-represented groups shown include both upregulated and downregulated transcripts (distributions not shown).

Functional Domains	Whole Cortex	Glutamate enriched	GABA enriched	Whole Cerebellum	Granule enriched	Purkinje enriched
Synaptic transmission	synapse	axon	synapse	glutamate receptor activity		neuropeptide signaling pathway
	synaptic vesicle		synaptic vesicle	neuropeptide signaling pathway
Protein trafficking & metabolism	SNARE binding	SNARE binding	clathrin-coated vesicle		protein autoprocessing	protein ubiquitination
	clathrin-coated vesicle	protein metabolism			peroxisome
		peptidase activity			protein binding
Signal transduction		signal transduction	MAPKKK cascade	calmodulin binding	calmodulin binding	MAPK signaling pathway
		calmodulin binding		second-messenger signaling	second-messenger signaling	second-messenger signaling
				protein kinase activity	protein kinase activity	basal transcription factors
Cytoskeleton- dependent processes	Rac 1 cell motility signaling pathway	axon cargo transport		actin binding	actin binding	actin binding
		cell motility		regulation of actin cytoskeleton	cellular morphogenesis	cell motility
		Rac 1 cell motility signaling pathway
Ion channels & ion homeostasis		ion homeostasis		voltage-gated potassium channel activity	calcium ion transport	ligand-gated ion channel activity
		magnesium ion binding		calcium channel activity
				calcium ion transport
Other				response to stress		cell adhesion
				citrate cycle		gap junction
						citrate cycle