Fig. 2
Genomic breakpoints in AciCCs correlate with active chromatin marks and NR4A3 binding sites at the 4q13 SCPP gene cluster. Summary of (top to bottom) mRNA expression (log2(FPKM)), gene loci (Genes), genomic translocation breakpoints (TXs), copy-number variations (CNVs), active (H3K27ac, H3K4me3) and repressive (H3K27me3) histone marks, NR4A3 binding sites, CTCF binding sites, DNA methylation, topologically associated domains (TADs), and chromatin contacts (HiC)10 for the chromosomal regions surrounding the 4q13 (left panel) and 9q31 (right panel) breakpoints in normal parotid gland and AciCC tumor tissues. mRNA expression is shown for ten AciCC tumors and three normal parotid gland samples in red and blue, respectively (Box-plot centre line: median; bounds of box: 25 and 75% quantiles; whiskers: extend to last value greater than Q1–1.5*IQR, and last value less than Q3+1.5*IQR respectively. Here IQR is the inter quartile range, Q1 is the first, and Q3 the third quartile). Black bars demonstrating the translocations correspond to genomic material included in the rearrangement, with red and blue bars indicating gains and losses, respectively. For each ChIP-seq experiment, ChIP signals (barcharts), as well as corresponding peaks (directly below ChIP signals) are shown. For H3K27ac, the super-enhancer peaks are shown in addition (purple). Furthermore, CTCF motifs within CTCF peaks are shown (below CTCF peaks). Blue arrows indicate motifs on the forward strand, whereas red arrows indicate motifs on the reverse strand. The DNA methylation tracks show the average methylation within 1 kb binned regions. Different TADs are indicated in different colors
