Fig. 4
Downregulated TEs are associated with specific histone marks and transcriptional-suppressed loci. Bubble plot of top ten ranked A) Cistrome Epigenome marks and B) Cistrome TFBSs associated to deregulated LTR elements. Bubble colour: -Log(p-value), as in legend. Bubble size: “support” percentage, expressed as the ratio between the number of intergenic differentially-expressed LTRs loci overlapping with Cistrome marker loci and the number of all intergenic LTR loci. C-G) Boxplots of GATA6 (C), ESR1 (D), TRIM24 (E), RAD21 (F) and STAG1(G) gene expression in 24 tumour and matched normal samples expressed as log2(normalized counts expression + 1). Paired t-test p-values are reported