Focusing on differences between D398 and N398 cultures, 1,194 genes were significantly different (≤1% FDR and at least 2-fold different, dashed lines; black dots in Fig. 3C). Taking the 349 genes that were relatively lower in N398, only two KEGG pathways were found to be enriched at relatively low confidence levels (blue bars in Fig. 3D), as determined by DAVID software3839. However, the 845 genes relatively increased in N398 were significantly enriched in Neuroactive ligand-receptor interaction, Ca2+ signaling pathway, and Axon guidance KEGG pathways (red bars in Fig. 3D). A selected sample of genes in this group is plotted in Supplemental Fig. 4H. Enrichment of GO functional groups similarly highlights neuron activity-specific biological processes (Supplemental Table 4). This predicts that N398 DA neuron cultures are likely to exhibit functional differences in response to ligand, potentially through changes calcium influx. This also suggests that the N398 variant may contribute to the excitatory response of neurons during nicotine exposure.
