Fig. 4

Using vissE to identify and characterise a proliferative phenotype in single-cell transcriptomic data of seven breast cancer patients from. a–c A uniform manifold approximation projection (UMAP) of cells from 7 patients annotated by a inferred cell types. b The projection of the fourth principal component (PC4). c Expression of the MKI67 gene that encodes the Ki67 marker of proliferation. d A gene-set overlap graph of gene-sets enriched in PC4 with nodes representing individual gene-sets and edges representing overlaps based on the adjusted rand index (ARI). Nodes are coloured based on the direction and significance of enrichment: green nodes represent gene-sets enriched in PC4 high cells. Six gene-set clusters representing biological themes are identified, containing 36, 76, 32, 7, 22 and 34 gene-sets respectively. e Cluster annotations generated by text-mining analysis of gene-set names. f Gene loadings (also known as weights) for genes belonging to gene-sets in the cluster plot against the number of gene-sets in the cluster the gene belongs to. g Protein–protein interaction (PPI) networks between genes that belong to gene-sets in the cluster. Each node represents a gene and edges represent known PPIs. Nodes are coloured based on gene loadings (also known as weight)