Gene set enrichment analysis of H3K27me3 marks. (A) Gene set enrichment analysis showing positive enrichment for H3K27me3 marks in genes which are down-regulated by the CDH1-knockdown model of EMT (P <0.0001). The bottom graph represents the rank-ordered, non-redundant list of genes. Genes on the far left (red) correlated the most with decreased gene expression following CDH1-knockdown. The vertical black lines show the position of each of the genes of the studied gene set in the ordered, non-redundant data set. The green curve is related to the enrichment score curve. (B) Gene set enrichment analysis showing positive enrichment for H3K27me3 marks in genes distinguishing luminal from basal like breast cancer (P <0.0001). (C) Pie chart showing that the majority of downregulated genes in the CDH1-knockdown model of EMT which gain H3K27me3 in Twist1-cells were also pre-marked by H3K4me3 in vector cells. FDR, false discovery rate; NES, normalized enrichment score.