Expanding the analysis to all genes, we note that the dendrogram and taxonomy (Figure 1C and Table S5) reflect systematic patterns of shared and unique gene expression. In order to understand what drives neuronal diversity, we collected the top ten most highly enriched genes in each neuronal cell type, reflecting both high expression and high specificity. A gene set enrichment analysis against the gene ontology (Figure 7A) (Huang et al., 2009) pointed to four clear categories of genes: those that establish cell identity (e.g., transcription factors, developmental genes), membrane conductance (e.g., ion channels, calcium-binding proteins), neurotransmission (e.g., neurotransmitter synthesis enzymes, transporters, neuropeptides, and their receptors), and synaptic connectivity (e.g., synaptic and cell junction proteins). These findings point to the specific functions that differ between neuronal types (connectivity, electrophysiology, and neurotransmission) and to the underlying regulatory machinery (transcription factors).
