Figure 3.

Comparison of genomic features among peak sets grouped by gene expression pattern. (A) The frequency of TBX20 DNA-binding motif identified de novo from ChIP-seq data (14). (B) The peak height was determined by the peak calling program QuEST (45) and is a proxy for the binding frequency or strength. The higher the peak height, more frequent binding was observed. (C) The frequency of peaks overlapping (±200 bp) with transcription start sites (TSS). (D) TBX20-binding region frequency per gene locus (regions/bp). (E) Conservation as measured by the phastCons algorithm (48). (F) Overlap with repeats. Asterisks indicate statistically significant differences (P < 0.05), compared with all expressed genes (A–D) or to sequences randomly selected from the genome (E and F). A description of the data presented in each panel and the statistical tests used are provided in Materials and Methods. Not expressed consists of the ‘no reads’ category. Results for the not expressed set with background levels were similar and are not shown for clarity sake (Supplementary Material, Fig. S6).