Fig. 1
From: Epigenetic landscape influences the liver cancer genome architecture
Hypo- and hyper-methylation of three paired hepatocellular carcinoma genomes. a In the upper panel, the left three plots show the methylation levels of the regions of tumor genomes (y-axis) or non-cancerous genomes (x-axis) delimited according to the 15 epigenomic segments. The color indicates the number of region. The orange plots show the density of LINE-1, purple plots show the density of transcribed regions, and green plots show the density of CpG islands. These densities were calculated for each fraction of the left three images, which were divided into 100 × 100 areas. In the lower panels, the genomic regions of the upper left three plots are shown separately for active and inactive chromatin state. b Methylation levels of tumor and non-cancerous genomes in the 15 epigenomic segments. The color indicates the number of bases. c Volcano plot of the differences in the methylation levels of CpG sites between tumor and non-cancerous genomes. Each dot represents a CpG site. Red indicates that the methylation level in the tumor genome is significantly (P < 0.05 using Fisher’s exact test) higher than in the non-cancerous genome, blue indicates lower, and gray indicates P ≥ 0.05. The x-axis indicates the log2 fold-change of the methylation level; the y-axis indicates the minus log10 of the P value
