Fig. 1
Cancer cells are characterized by reduced H3K9me3 level at satellite elements compared to normal cells. a Two-dimensional PCA plot of cell lines based on H3K9me3 enrichment at autosomal satellite elements. Ellipses define 95% confidence intervals around group mean. b Heatmap (based on scaled log2-transformed FC values) representing H3K9me3 enrichment of 382 differentially enriched satellite elements on autosomal chromosomes shows clustering of normal versus cancer cells, with an exception of PBMC and Dnd41. Names of normal cell lines are in blue; cancer cells are in red. c Density plot of calculated fold change (ChIP over input) for normal and cancer cell lines at 407 differentially enriched satellite elements (p-value < 0.05; Welch two-sample t-test). Averages are shown by dashed lines. d Density plot showing fraction of zero quality mapping reads at satellite elements with differential enrichment of H3K9me3 between normal and cancer cell lines. Density plots are shown for two replicates of HMEC and A549 cell lines