Fig. 2

Differentially expressed genes are enriched at cell-specific genomic compartments. a Scatter plot showing differential gene expression between MCF-10A and MCF-7 cells. The axes represent normalized RNA-seq log2 gene expression counts. Red dots denote genes whose expression changed significantly and grey dots denote genes whose expression was unchanged. b Heatmap showing the MCF-7 up- and down-regulated genes for each biological replicate. Differential expression analyses identified 2437 MCF-7 up-regulated and 2427 MCF-7 down-regulated genes (log2 fold change > 1, p < 0.01) with high reproducibility. c MCF-7/MCF-10A log2 fold change expression boxplot of all the genes residing at regions for different compartmental switch categories. The compartments that are A → B and B → A show significantly decreased and increased expression levels, respectively. The p valuewas determined with Wilcoxon rank-sum test