Fig. 3

Using vissE to identify and characterise biological themes observed in an epithelial to mesenchymal transition (EMT) in the human mammary epithelial (HMLE) cell line. a A gene-set overlap graph of gene-sets enriched during an EMT 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 mesenchymal cells and blue in epithelial cells. Four gene-set clusters representing biological themes are identified, containing 14, 104, 31 and 34 gene-sets respectively. b Cluster annotations generated by text-mining analysis of gene-set names. c Log fold-change (logFC) of genes belonging to gene-sets in the cluster plot against the number of gene-sets in the cluster the gene belongs to. d 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 the logFC