Fig. 5

Analysis of the prefrontal cortex spatial transcriptomics data. A Spatial coordinates and layer annotations of the cortex data. B Type I errors of SpatialDE, SPARK, SPARK-X, MERINGUE, and spVC in the permutation analysis. C Number of significant genes whose expression was up-regulated in each of the six neocortical layers compared with the white matter. D Number of significant genes whose expression was down-regulated in each of the six neocortical layers compared with the white matter. E Relative expression levels of six example genes with significantly higher expression in L1 to L6 layers, respectively. The top row shows all spots and the bottom row only shows spots in the corresponding layers and WM . The read counts were normalized by library size, log-transformed, and then scaled by the min-max normalization to obtain the relative expression levels