Figure 5.

Network analyses of dynamically regulated transcription factors (TFs) in differentiating cortical excitatory neurons, derived from the IPA-Ingenuity Network Tool (see Methods). a, ≥ 3 fold up- and ≥ 3 fold down-regulated TFs were imported along with endogenous chemicals (e.g., retinoic acid) to populate the network. Grey boxes collect the up-regulated genes expressed in the “upper,” “mid” and “deep” cortical regions (CP + MZ, IZ, VZ alone) as well as the down-regulated genes (VZ) and the group of IPA Interacting Genes. Gray lines that are numbered indicate interactions between cortical zones (upper, middle, and deep); light blue lines indicate direct interactions of upper, middle, and deep up-regulated genes, and down-regulated genes, with IPA interacting genes. Dark blue lines indicate interactions between IPA interacting genes (see Results). b, Tabular summary of interactions between cortical zones. 1, Interaction identified by IPA Ingenuity analysis.