ΔDNase regions are associated with androgen receptor-regulated transcription. (a) Heatmap of mRNA-seq expression levels (natural log of reads per kilobase mapped expression value) for genes identified as differentially regulated by the AR. Rows are ordered by total sum. Genes most commonly identified in microarray studies as AR-regulated are all located near the top of the heatmap, indicating overall high levels of expression before and after hormone induction. (b) ΔDNase changes randomly permuted against mRNA-seq identified up- and downregulated genes. ΔDNase regions were mapped to the closest gene, and the amount of overlap between these genes and the differentially expressed set was permuted 100,000 times to assess significance. Arrows indicate the actual overlap between ΔDNase nearest genes and mRNA-seq regulated genes relative to random permutations. Blue shading represents less ΔDNase regions (absence/depletion) around regulated genes than expected by chance. Yellow shading represents more ΔDNase regions (presence/enrichment) present around regulated genes than expected by chance. AR: androgen receptor; mRNA-seq: messenger RNA abundance measured by high-throughput sequencing.
Tewari et al. Genome Biology 2012 13:R88 doi:10.1186/gb-2012-13-10-r88