Figure 2

Expression level of nearby genes of the HSEL and MSEL. (A) Number of genes with cell type specific enhancer loci (i.e. HSEL, MSEL) from top 300 overexpressed genes in MDAMB231 (blue), top 300 overexpressed genes in HMEC (red), and three randomly selected 300 gene datasets as controls (orange). The enrichment of genes with cell type specific enhancer loci in each group was calculated by performing chi-square test between groups. (B) Log fold change of nearby gene expression boxplot for the HSEL and MSEL (in windows of 100 kb). Student t-test was applied between groups in order to calculate p-values. Nearby genes of cell type specific enhancer loci (HSEL (C), MSEL (D)) were categorized to three groups; overexpressed genes in MDAMB231 (blue), overexpressed genes in HMEC (red), and no change in gene expression (green), and fraction of genes for each category was graphed. Eight different window sizes were used for the nearby gene distance from cell type specific enhancer loci: from 20 kb windows of cell type specific enhancer loci (±20 kb of HSEL/MSEL) up to 2 Mb windows (±2 Mb of HSEL/MSEL).