Fig. 2.

Spatial gene expression heterogeneity within the 1.2 cancer tissue sample. a Factor activity maps for selected factors corresponding to epithelial, stromal, cancerous, PIN, or inflamed regions. Remaining factors’ activity maps in Supplementary Figure 2 and Supplementary Data 1. b Annotated brightfield image of H&E-stained tissue section. c Heatmap of the 20 most variable genes between cancer, PIN and normal gland regions, using spot sets from Supplementary Fig. 4b. Centered rlog: difference of rlog (variance-stabilized transform of ST expression data) and gene-wise mean rlog. Arrows highlight genes of interest validated by immunohistochemistry (IHC). d First two principal components of spot sets from c separate cancer, PIN and normal regions. e Array dot plots for SPINK1 and NPY. Circle size in array dot plots indicates normalized ST counts. f IHC staining for SPINK1 and NPY of an adjacent section on the ST array. Nuclei are stained with DAPI (blue). Scale bar indicates 1 mm