Figure 4: Networks of looping interactions.
From: The long-range interaction landscape of gene promoters
a, Histogram showing the number of TSSs (left, red) or distal fragments (middle, blue) in percentages that are involved in 0, 1, 2,….10 (and above) looping interactions (degree, x axis) in GM12878 cells. All of the values for degrees that are >9 are grouped under degree 10+. The dark red bars represent the percentages of looping TSSs that are expressed whereas light red bars represent the percentages of looping TSSs that are not expressed. Inset: the difference in percentage between looping TSSs that are expressed and not expressed for each degree is shown. The right panel shows the degree distribution for each functional group of distal fragments. The average degrees (mean, μ) for TSSs and distal fragments are indicated. The first value is the mean degree considering all the TSS/distal fragments (looping plus non-looping), whereas the second value is the mean degree of looping TSS/distal fragments (excluding degree = 0). b, Web plot showing the long-range looping interactions in the ENr132 region in K562 cells. The interrogated distal fragments (blue circles) and the TSSs (red circles) are positioned according to genomic coordinates and the GENCODE v7 gene annotation is indicated. The size of the red circles indicates whether that TSS is expressed (large circles) or not expressed (small circles). The thin grey lines show all the interactions that were interrogated. The coloured lines show significant looping interactions between TSSs and distal fragments of a particular group.
