Fig. 3

HAR-BRAIN gene expression. a Cortical gene expression of HAR-BRAIN genes. b Cortical maps of the significance level obtained by permutation tests, comparing expressions of HAR-BRAIN genes to equally sized random gene-sets taken from BRAIN (NULL1) and ECE genes (NULL2). c Association between the gene expression profile of HAR-BRAIN genes and normalized cortical expansion between human and chimpanzee (left). The correlation coefficient is significantly higher than NULL1 and NULL2 (both p < 0.001, two-sided, permutation test; right). d HAR-BRAIN gene expression within each of the seven functional networks ranked in descending order of the mean expression. Asterisks (*) indicates significantly upregulated regions as in panel b. e HAR-BRAIN gene expression in cognitive networks (DMN, FPN, and VAN) versus the SMN and VN (left), with permutation results demonstrated in the right panel (two-sided p = 0.003 and p < 0.001 for NULL1 and NULL2, respectively). f HAR-BRAIN gene expression in the DMN versus the rest of the cortex (left), with permutation results demonstrated in the right panel (two-sided p < 0.001 for both NULL1 and NULL2). g Species-homologous brain areas as presented in the PsychENCODE dataset for the human (left), chimpanzee (upper right), and macaque (lower right). h Normalized expression levels of HAR-BRAIN genes in regions of higher-order networks compared to areas of the SMN/VN in humans (p < 0.001, two-sample t test). Largest differences in gene expression are found in humans, with chimpanzees in second place, followed by macaques (p = 0.002, Jonckheere-Terpstra test). Asterisks (*) indicates two-sided p < 0.05, FDR corrected. Central marks denote the mean gene expression. Boxplot center, median; box = 1st−3rd quartiles (Q); lower whisker, Q1–1.5 × interquartile range (IQR); upper whisker, Q3 + 1.5 × IQR. Colors indicate the assignment of functional networks, as in Fig. 2b. M1C primary motor cortex, S1C primary sensory cortex, IPC inferior parietal cortex, STC superior temporal cortex, ITC inferior temporal cortex, A1C primary auditory cortex, OFC orbital frontal cortex, VFC ventral frontal cortex, DFC dorsal frontal cortex, V1C primary visual cortex, MFC medial frontal cortex. Source data provided as Source Data file