Supplementary Figure 6: SpatialDE applied to breast cancer biopsy tissue.

(A) Corresponding HE image of breast cancer tissue from spatial transcriptomics. (B) Fraction of variance explained by spatial variation (x-axis) versus SpatialDE negative log P-value (y-axis) for all genes. Dashed line corresponds to the FDR=0.05 significance threshold (N=115 genes, Q-value adjusted). Genes classified as periodically variable are shown in orange (N=22), genes with a general spatial dependency in blue (N=93). Disease-implicated genes annotated based on prior knowledge (Stahl et al.⁶) are highlighted with red labels. Other representative genes are annotated with black labels. The X symbol shows the result of applying SpatialDE to the estimated total RNA content per spot. (C) Visualization of 37 selected spatially variable genes with different periods and length scales. The black scale bar corresponds to 1 mm. Colors and labels as in (Fig. 2). Stars next to gene names denote significance levels (* FDR < 0.05, ** FDR < 0.01, *** FDR < 0.001, Q-value adjusted) of spatial variation.