Fig. 2: cisTOPIC identifies 16 clusters of cells spanning 30 topics from 14,251 cells.
From: Epigenetic loss of heterogeneity from low to high grade localized prostate tumours
a Single-cells from 18 prostate samples were clustered using cisTOPIC based on their chromatin accessibility profiles. Cells are coloured according to their sample IDs on the UMAP. b Single-cells from 18 prostate samples formed 16 clusters based on their shared chromatin accessibility profiles. Cells are coloured according to their cluster IDs on the UMAP. c Heatmap showing the topic distribution across 16 clusters. d Epithelial and stromal cell types are identified in localized prostate tumours. Lymphoid, myeloid and fibroblasts (grey tones) are removed from downstream analyses. Outer clusters show high-MYC accessibility (blue tones). The middle cluster shows higher accessibility to genes associated with inflammatory response (red tones). e Gene scores are shown for epithelial cell type markers luminal (KRT8), basal (KRT5 and KRT14) and neuroendocrine (Chromogranin A); common prostate epithelial cell markers AR, TMPRSS2 NKX3.1; prostate cancer cell markers AMACR, EPCAM, CDH1, C-MYC and PTEN.
