Extended Data Fig. 15: Biological pathways explained by subclone or tumor density.

a, Subclone-associated pathways identified through gene set enrichment analysis. b, Hallmark E2F target genes (n=200) plotted according to percent variance explained by clonal identity (x-axis) and tumor density (y-axis). Included genes colored by normalized density on the scatter plot, all other genes are shown in grey. c, Expression of highly subclone-associated E2F target genes (n=11, listed in a), plotted for spatial tumor regions of the slide-RNA-seq array from Fig. 4. d, MYC target genes (n=200) plotted according to percent variance explained by clonal identity (x-axis) and tumor density (y-axis). Included genes are colored by normalized density on the scatter plot, MYC is colored red, all other genes are shown in grey. e, Expression of highly subclone-associated MYC target genes (n=16, listed in a), plotted for spatial tumor regions (left). Box plot showing normalized MYC target gene expression by subclone assignment; each point represents a spatial tumor cluster (right). Red line, mean, red box, 95% confidence interval for mean, blue box, standard deviation. f, MYC expression plotted for spatial tumor regions (left). Scatter plot showing normalized MYC expression by tumor cell density; each point represents a spatial tumor cluster (right). g, Subclone-associated pathways identified through gene set enrichment analysis. h, Cell adhesion molecule binding genes (n=514) plotted according to percent variance explained by clonal identity (x-axis) and tumor density (y-axis). Included genes are colored by normalized density on the scatter plot, all other genes are shown in grey (reproduced from Fig. 4i). i, Expression of highly density-associated cell adhesion molecule binding genes (n=14, listed in g), plotted for spatial tumor regions. Scale bars, 500 μm.