including genes differentially expressed across these layers (5494 genes; ANOVA p<0.01, Benjamini-Hochberg adjusted). Gene list characterizations were made using a combination of module eigengene / representative gene expression, gene ontology enrichment using DAVID60, and enrichment for known brain-related categories (i.e.,61,62) using userListEnrichment63. Module C31 is depicted using VisANT64: the top 250 gene-gene connections based on topological overlap are shown, with histone genes removed for clarity. Rostral-caudal areal gradient genes were identified as follows: first, the center of each neocortical region was identified at 21pcw in Euclidean coordinates; second, the rostral/caudal region position was estimated as an angle along the lateral face of the brain centered at the temporal/frontal lobe juncture (ordering lobes roughly as frontal, parietal, occipital, temporal; Fig. 5c); third, for each brain gene expression in each layer was (Pearson) correlated with this region position; and finally, genes with R>0.5 in all four brains were identified. A similar strategy was used to identify unbiased areal gradient genes (Suppl. Methods). Enrichment of haCNSs was determined using hypergeometric tests. Samples in all plots are ordered in an anatomically relevant manner. Unless otherwise noted, all p-values are Bonferroni corrected for multiple comparisons.
