Figure 4: CAGE data show downregulation of TSS activity after the break.

(a) Coverage profile plot representing the RPM of CAGE reads in induced (blue) and uninduced (red) samples at TSSs of genes (n=196) with cut AsiSI sites in a 500 bp window. TSS, transcription start site. Bold lines represent mean values, whereas semi-transparent shades around the mean curves represent the s.e.m. across the regions. (b) Promoter-centred expression profiling. Comparison of expression coverage profiles for TSS activities between uninduced and induced samples. Promoters are grouped into expression classes by applying k-means clustering. Each box represents one cluster with reported above the total number of promoters and in brackets the number of overlapping cut AsiSI sites. Individual beanplots show distribution of scaled normalized expression for uninduced and induced samples. Colour of the beanplots represents the different expression classes of TSS dynamics: downregulated TSSs in green; upregulated TSSs in yellow; nearly unchanged TSSs in grey. Individual CAGE experiments (uninduced or induced) are shown on x axis and scaled normalized expression on y axis.