Figure 3

Histogram of distance to the nearest TSS and of peak lengths. (A) The distribution of distance to the nearest TSS. This example is of the transcription factor binding sites for ATF2. The x-axis of the histogram is centered at 0 and divided into 100 bins that cover the largest and smallest values of distance. As shown in this histogram, most of the binding sites are located near the TSS. The exact number of peaks for each range of distance appears when the mouse pointer hovers over that bar. (B) The distribution of the peak lengths of transcription factor binding sites of ATF2. Most of the peaks have a length smaller than 600 bp. Again, if users are interested in the exact number of peaks within each range, hovering over that range will reveal the value. (C) The user may use filter criteria to select a subset of peaks. There are two ways to filter the peaks (highlighted by the red boxes). The first is the slider bar and the second is the text box. In this example, we use text boxes to filter out peaks with distance to the nearest TSS larger than +200 or smaller than -200. After this operation, 2,847 peaks are left. After the selection step, the histogram is refreshed with this subset of peaks in real time. After this filter step, we save the filtered subset with the “save” button above the histogram.