Fig. 5

Fig. 5

a Elbow plots for each histone modification following allocation of the genome into 3.1 million consecutive bins of 1 kb. The example shown is for adrenal providing the number of reads per bin at the point of maximum gradient change (the elbow point, red dot) and a quantitative measure of whether a bin was marked or not (e.g., >10 or <10, respectively, for H3K27ac). Converting marks into a binary yes/no call at any point in the genome facilitated the data integration across the different tissues. While the number of reads per bin at the elbow point was different for each mark across the tissues, the shape of the curve remained the same. b Euler grid for bins marked by H3K27ac (defined by elbow plots) in replicated tissues (i.e., two rows/replicates per tissue). Total number of marked bins per individual dataset is shown to the right. The example in (b) required a bin to be called in any two or more samples and is ordered by decreasing bin count per pattern (bar chart above the grid). A total of 48,570 different patterns were identified, of which the top 40 are shown. Tissue specificity for all sites emerged in the top 265 (0.5%) patterns; colour-coded asterisks above columns). For example, nearly 14,000 bins marked only in the two Heart/LV H3K27ac datasets ranked first as the most frequent pattern. The seventh most frequent pattern in ~3000 bins was palate-specific. Tissue-specific patterns were far less apparent at promoters (H3K4me3, n = 18,432; Supplementary Fig. 10) or for H3K27me3 (n = 26,339; Supplementary Fig. 11). While patterns across multiple tissues were permitted by stipulating marks in ≥2 samples (e.g., heart and adrenal in column 24), they could be enforced by stipulating marks in at least four samples (Supplementary Fig. 12). c Enrichment of known TF-binding motifs in the tissue-specific patterns of H3K27ac identified in (b). Five individual tissues are shown as examples alongside analysis of the shared regulatory pattern identified for the limb and palate identifying marked enrichment of a compound PITX1:E-box motif. Motif-enrichment was conducted using a one-sided Binomial test implemented in findMotifsGenome.pl of the HOMER package.