Multiple-scale clustering of transcription initiation events. (A) Clustering of transcription initiation events in a 9-kb region around the JUN oncogene in human chromosome 1. (B) Zoom-in on the main JUN promoter region. Each panel displays genomic features with a representation similar to that used by the UCSC Genome Browser (Kent et al. 2002). Different types of features are shown in different “tracks,” stacked from top to bottom in each panel. The topmost track shows the location in chromosome 1. Below this, the next track indicates the location of the single-exon JUN gene, according to RefSeq cDNAs in the UCSC database (Karolchik et al. 2003); the thicker part with chevrons is the protein-coding region, and the thinner parts are the 5′ and 3′ untranslated regions. Transcription is directed right-to-left. CpG island regions are shown below. The CAGE track (the first barplot) shows the number of CAGE tags initiating from each nucleotide. There is clearly a cluster of initiation events roughly covering the JUN gene, contrasted with a striking absence of initiation events on either side of the gene. Furthermore, this cluster clearly contains a much denser subcluster in the annotated promoter region, and the subcluster seems to contain a core region with an even greater density of initiation events (B). The clusters track (B, bottom) shows the clusters in the CAGE data picked out by our algorithm. Stable clusters (stability ≥2) are black and unstable clusters are gray. Only clusters >1 nt are shown in this track. For some of the clusters in this track, we only see one of their ends, as they extend further in the 3′ direction. Finally, the cluster-stability track shows these same clusters as blocks that are stacked on each other, where the height of each block reflects the cluster’s stability. (In fact, the logarithm of the d parameter from our algorithm is plotted on the Y-axis, so that the height of each block is proportional to the logarithm of the cluster’s stability. See the main text and Methods for definitions of stability and d.)