Fig. 6

The 55 genes identified in Alb-R26^Met tumours are also upregulated in the H⁺E⁺ patient subset, and a large proportion of them is characterised by hypermethylated CGIs. a Heat-map reporting expression levels of genes found overexpressed and with hypermethylated CGIs in Alb-R26^Met tumours versus control livers (rows; subdivided in Group I and II and organised according to the relative position to the ATG) in individual HCC patients (columns; organised as in Fig. 5a). Red: upregulated genes; green: downregulated genes. Black: not differentially expressed. White: data not available. The scale is shown on the right (expressed as Log₂ FC). The H⁺E⁺ patient subset is highlighted in orange (left), whereas all other patients in green (right). b In the graph, each dot corresponds to a given gene (the total 51 genes are reported). Their position corresponds to the percentage of patients in which the gene is overexpressed. In orange (left), for the H⁺E⁺ patient subset. In green (right), for all other patients. c Unrooted distance tree of HCC patients based on the 51 genes identified in the Alb-R26^Met tumours. In orange: H⁺E⁺ patient subset. In green: all other patients. d Heat-map highlighting with a yellow square genes overexpressed and with hypermethylated CGI in the corresponding HCC patient. The heat-map is organised as in panel A. Black square: genes not simultaneously overexpressed and with hypermethylated CGI in the corresponding HCC patient. Grey: data not available. e Tables reporting the numbers with percentages of genes overexpressed and with hypermethylated CGI in at least 1, 5, 10 or 20 HCC patients (left), as well as numbers with percentages of patients with at least 1, 5, 10 or 20 genes overexpressed and with hypermethylated CGI out of the 55 genes identified in the Alb-R26^Met model (right). f Histogram reporting the KEGG pathway enrichment analysis for the 55 genes identified in Alb-R26^Met tumours, ordered according to the −Log₁₀P-value. Significance is indicated on the top. ***P < 0.001