Distribution of the six types of regions in the genome in K562. (a) Densities of the regions in the whole genome, defined as the running fractions of bases covered by the regions. The tracks are, respectively, from outermost to innermost, the ideogram for the human karyotype (genome build hg19), Gencode version 7 level 1 and level 2 genes, BARs, BIRs, PRMs, DRMs, HOT regions and LOT regions. The tracks are scaled separately to show density fluctuations. The highlighted segment corresponds to the area in (b). (b) Zoom-in of chromosome 3 to show the correlated fluctuations of the different types of regions. (c) Locations of the six types of regions at the beginning of the q-arm of chromosome 22 in K562. Due to the high density of genes, only a subset of the gene names is shown. Expression values were measured by long poly-A+ RNA-seq of whole-cell RNA extract. A darker color indicates a higher average expression level in the local region. Box i marks a broad area with significant active TF binding and co-binding. Box ii marks an area with many small interspersed active and inactive TF binding regions.
Yip et al. Genome Biology 2012 13:R48 doi:10.1186/gb-2012-13-9-r48