Fig. 3: Spatial variations of gene expression across the cortex.

a, Three models of differential gene expression across cortical areas. H2 types are indicated by cell shape; cool-toned shapes indicate H2-type-specific genes; warm-toned shapes indicate area-specific genes in model 2 and H3-type-specific genes in model 3. b, Expression of selected spatially variant NMF modules plotted on cortical flatmaps. c, Expression of selected marker genes in each NMF module. d, Histogram showing the number of areas (out of 37) in which an H3 type was detected: an H3 type was considered present in an area if that area contained at least 3% of that H3 type. e, Spatial distribution of example L4/5 IT and L5 ET H3 types across the cortex plotted on cortical flatmaps. Colours indicate relative cell count in each cubelet; grey lines delineate cortical areas. f, Distribution of L4/5 IT H3 types in an example coronal section. Dashed lines indicate area borders in CCF. Magnified views of dashed boxes are shown on the right. Brackets indicate barrels in the barrel cortex. g, Cortical areas defined in CCF (left) and those predicted by H3 type (middle) and cubelet gene expression (right). h, Fraction of correctly predicted cubelets using H3-type composition, cubelet gene expression and shuffled control. Each box shows the performance of n = 100 resampled trials. Boxes show median, and quartiles and whiskers indicate range after exclusion of outliers. Dots indicate outliers. i, Matrix showing the AUROC of pairwise classification between combinations of cortical areas. Areas are sorted by modules, which are colour coded on the left. The dendrogram was calculated using similarity of H3-type composition; clusters were obtained based on the matrix and are shown in the grey-bordered boxes. j, Cortical flatmaps coloured by cell-type-based modules (left) and by connectivity-based modules identified by Harris et al.³ (right).