Finally, we identified a module (C31) with particular enrichment in SG and VZ (Fig. 3b, upper right), containing many interneuron-associated genes (Fig. 3c). DLX1 and DLX2, homeobox transcription factors essential for interneuron migration and survival10, were central ("hub") genes therein. There is controversy regarding the origin of cortical interneurons in primates, where the argument has been made that a substantial proportion of interneurons are generated locally in the VZ12,13. However, several recent studies have shown strong evidence that, as with rodents, primate interneurons are generated extracortically in the GEs11,14. To address this issue, we generated a new network using neocortical as well as GE samples, and examined the distribution of C31 genes therein. Most genes were assigned to a module showing common enrichment in both the GEs and VZ (Extended Data Fig. 6). While this finding does not resolve the origin of cortical interneurons, it shows that transcriptional programs associated with these cells in both structures are highly similar.
