Supplementary Figure 3: Gene expression conservation across cortical layers among three species.

(a) The number of genes with section-related expression in each species based on DS1 (humans – red, chimpanzees – green, macaques – blue). (b) The PCC distribution based on the gene expression of section-related genes between each pair of species in DS1: brown – human and chimpanzee, green – chimpanzee and macaque, purple – human and macaque. The section-related genes were defined as genes with section-related expression in at least one species (upper panel), or genes with section-related expression in all three species (lower panel). (c) The PCC distribution based on the gene expression in DS1 human samples and the human ISH data. The gray bars show the chance PCC distribution estimated by permutation of gene labels 1,000 times. (d) Expression of macaque layer markers (MLMs) in human and chimpanzee cortical sections. The MLMs include known MLMs identified based on LCM samples of individual cortical layers (L2-L6) and the novel MLMs. The columns show the average relative expression levels of MLMs specific to a given layer in humans or chimpanzees, as marked by the silhouette figures. The darker shades of blue represent higher relative expression across sections. The gray scale bar shows section labels. The darker shades of gray represent deeper cortical sections. The black boxes and white labels show the cortical sections assigned to the cortical layers marked by the layer markers and white matter markers. The median expression fold change (the median difference between maximum and average expression levels in depicted laminar sections) and its 5%-95% range are shown on top of the heatmap panels.