Fig. 5

Heatmaps of chromatin, DNA and transcript features at enhancer candidates. DNase I hypersensitivity, H3K9ac enrichment, mCG, mCHG and mCHH levels, presence of TEs and transcript levels at and around (±1 kb) DHSs in enhancer candidates. DHSs were scaled to equal size. The colour scales are in RPM for DNase I hypersensitivity, H3K9ac enrichment and transcript levels, and in methylation frequency (0–1) for DNA methylation. For TE sequences, red and white show the presence or absence of TEs, respectively. DHSs were clustered based on H3K9ac enrichment using a k-means (k = 4) clustering algorithm. The categories identified were numbered from 1 to 4 from the top to the bottom. All the DHSs were oriented based on H3K9ac enrichment intensity values 300 bp away from the DHS boundaries; the side with higher H3K9ac enrichment was defined as 3' end