Transcription factor clusters are strongly enriched around transcription start sites (TSSs) in actively transcribed genes. (A) Mapping of transcription factor clusters around TSSs in annotated genes and promoters for transcribed and silent genes in K562 and Gm12878. Bars correspond to the number of clusters within 200-bp intervals. The dotted line indicates the same level in both graphs and is included to emphasise the difference in axis scales between transcribed and silent genes. (B) Percentage of clusters identified as promoter clusters (mapping within 2,000 bp upstream and 200 bp downstream of TSSs) and gene clusters (mapping within 10 kb upstream of TSSs or within the gene body but outside the annotated promoter region). A substantial number of gene clusters mapped to transcribed and silent genes in both cell lines.