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Fig. 5 | Genome Biology

Fig. 5

From: Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

Fig. 5

DNA methylation analysis. A Heatmap of all significant CpG islands differentially methylated across the MIKK panel samples. CpG islands are sorted by genomic positions and the X-axis. Samples are ordered by hierarchical clustering on the Y-axis and color coded so that sibling lines are indicated with the same colors. The color scheme is according to the value of the median log-likelihood ratio from −3 (blue) to 3 (red) with ambiguous values between −1 and 1 in white. B Distribution of distances to the closest gene TSS for significantly differentially methylated CpG in red (n=4249) and all non-significant islands in blue (n=8727). C Number of significant CpG islands by genomic windows for the 24 HdrR chromosomes, from 0 (white) to 6 (dark red). D Example 100kb region containing a significant CpG island in red (chr15:1565040-1565987) as opposed to non-significant ones in white. E CpG level log-likelihood ratio kernel density plot for the CpG island highlighted in panel D. Samples are sorted on the Y-axis by decreasing median llr. Individual CpG values are indicated by dots. F Heatmap of log-likelihood ratio with hierarchical clustering by sample for the CpG island highlighted in panel D. On the X-axis are individual CpGs sorted by genomic position

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