Figure 3
Integrated analysis of the ChIP-seq and RNA-seq data. (A) Correlation of RA gene regulation (log2 fold change of expression RA versus DMSO) according to the number of neighbouring RARaa ChIP-seq peaks. Only RA-regulated genes were included in the plot. (B) Venn diagram showing the overlap of genes harbouring nearby RARa binding sites (yellow) and those up-regulated by RA (purple), or down-regulated by RA (blue). The below panel also shows the overlap with the genes down-regulated by BMS493 (red). The 13 genes showing up-regulation by RA, down-regulation by BMS493 and harbouring a RAR site are tshz1, nr6a1b, foxg1b, nr2f5, gata6, dhrs3a, hoxb1b, slc22a3, ppm1h, nrip1a, col7a1l, hoxc1a and hoxb5b.
