Fig. 3

Integration of ChIP-seq data and gene-expression data. a Examples of gene expression arrays performed. Shows (a) upregulation of BRD1-S vs. control, (b) upregulation of BRD1-L vs. control, (c) siRNA downregulation of BRD1 vs. control, and (d) two controls transfected with scrambled siRNA, control 1 vs. control 2. The red lines indicate fold change 1.5 which was used in this study to identify DEGs. The number of upregulated and downregulated DEGs is shown for each study in the upper left and lower right corner, respectively. Three siRNA knockdown experiments of BRD1 (KD1-3) were performed. More information about KD1-3 can be found in Additional file 10. e The number of genes that overlap after upregulating BRD1-S and BRD1-L expression. After upregulating either BRD1-S or BRD1-L, the number of DEGs was identified in 10 kb segments (blue bars) across a window of +/– 200 kb from either (f) BRD1-S or (g) BRD1-L binding sites, respectively. The expression fold change quartiles were obtained from segments of 10 DEGs. Gray areas indicate the upper and lower quartiles while the middle is shown as a gray line