Fig. 3

Example ColoWeb output: comparison of the distribution of K562 replication origins to K562 histone modification H3K4me3. The x axis represents distance from the center of a replication origins or b randomized regions. Each scatterplot contains 100 rows. Each row contains data for 50 randomly selected regions [origin-containing regions in (a) and randomized fragments of the same GC content in (b)], divided across 100 bases bins. The grayscale corresponds to the extent of H3K4 trimethylation in each bin. c, d Graphs summarizing the colocalized peaks for the analyses represented in (a, b), respectively. The green horizontal lines for the mean and high/low oscillation values (40th and 60th percentiles, respectively) are shown on the histogram. The shaded area, covering the region under the peak and above the upper variance level [48], corresponds to the above mean integral (AMI) used in colocalization studies. For more examples of scatterplots, see Additional file 1: Fig. S3