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Fig. 2 | Journal of Translational Medicine

Fig. 2

From: Age-associated hydroxymethylation in human bone-marrow mesenchymal stem cells

Fig. 2

Chromatin signatures associated with DNA hydroxymethylation in MSCs. a Heatmap showing the relative enrichment of the frequently hydroxymethylated (FhmC) sites for several combinations between ENCODE Broad Histone project cell lines and histone marks. A red tile is drawn only if the 5hmC site is significantly enriched for the corresponding combination (Fisher’s exact test; p < 0.05); a white to red scale is used to represent the strength of the enrichment, using the base-2 logarithm of the odds ratio (OR) as a measure of the shift size. b Upper: Circular layout of chromosomes 6 and 17. Outermost track: Tile chart describing the location of the FhmC sites. CpG locations were enlarged to 200 kbp regions centered on the site of interest to enhance the visualization. Middle and innermost tracks: Histogram charts showing the peak scores obtained from the Broad Histone UCSC data for H3k4me1 (middle) and H3k9me3 (innermost) averaged over 200 kbp regions. Lower: Genome diagrams showing the relative enrichment of H3k4me1 and H3k9me3 marks on two specific regions of chromosomes 17 (left) and 6 (right) and the FhmC sites. c Heatmap showing the relative enrichment of FhmC sites for given sets of combinations between ENCODE Broad ChromHMM project cell lines and chromatin states. A tile is drawn only if FhmC sites are significantly enriched for the corresponding combination (Fisher’s exact test; p < 0.05). Tile colors are chosen to resemble those used in the UCSC representation of the ChromHMM dataset. The intensity of the color is used to represent the strength of the enrichment, using the base-2 logarithm of the OR as a measure of shift size

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