Fig. 9

Early transcriptional changes imposed by HBV-infection in vitro persist in HBV-related HCC patients. a) Heatmap of the 100 ATAC-Seq/RNA-seq co-regulated genes that are differentially expressed (71 down- and 29 up-regulated) in the in house Lyon cohort of matched HBV-related HCCs (T; magenta) and Non-Tumor (NT; green) tissues (n = 10). Normalized counts are represented with a color scale from blue (negative) to red (positive). b) KEGG pathways (Release 86.1; yellow bars) and HALLMARK MSigDB modules (blue bars) significantly enriched from the 100 genes differentially expressed in the in-house Lyon cohort of matched HBV-related HCC samples (T vs NT; full bars) and the 57 genes differentially expressed in TCGA-LIHC subset of matched HBV-related HCCs (T vs NT; striped bars) (ShinyGO 0.76 tool) and sorted by–Log (FDR) values. Fold enrichment ranks the relative number of genes included in each enriched pathway (see Tables S15 and S11). c) Heatmap of the 57 ATAC-Seq/RNA-seq co-regulated genes that are differentially expressed (43 down- and 14 up-regulated) in the TCGA-LIHC subset of matched HBV-related HCCs tissues (n = 6; T: magenta and NT; green). Normalized counts are represented as in a). d) Kaplan–Meier curves generated comparing the 14/57 up-regulated genes (left panel) and the 43/57 down-regulated genes (right panel) in the whole TCGA-LIHC