Overlap of transcription initiation clusters from different cell lines. (A) Overlap between clusters from skin fibroblasts (HBM library) and clusters from HepG2 cells (HBY library). (B) Overlap between clusters from skin fibroblasts (HBM library) and clusters from cerebrum (HAM library). If two clusters overlap, the degree of overlap is measured as the number of nucleotides in the intersection of the clusters divided by the number of nucleotides in the union of the clusters. This value varies between one (perfect overlap) and zero (no overlap). Since we are dealing with nested hierarchies of clusters, it is not appropriate to compare every cluster from one cell line with all overlapping clusters in the other cell line. In each panel, the first mentioned library is designated as the “query,” and the second as the “reference.” For each query cluster, we wish to know whether there is a closely corresponding reference cluster. Only robust query clusters are considered, i.e., those with stability ≥2. For each query cluster, we find the reference cluster with the highest degree of overlap, and report this value. If there is no overlapping reference cluster, an overlap value of zero is reported. Cases with an intermediate degree of overlap are often caused by single, outlying CAGE tags that shift the cluster boundary in one library.