Fig. 2

PMD signatures discriminate cell type and global transcriptional control. a Colored representation of the emission probabilities calculated by ChromH3M. Samples and states were hierarchically clustered forming six main groups: myeloid, lymphoid, endothelial, liver, digestive system, and heart. Beneath each sample, the corresponding average methylation levels within PMDs is shown as whisker box plots and the percentage of MethylSeekR segments as stacked bar plots. Samples derived from the same cell type clustered together, although they differ in mean methylation level, suggesting that they have more similar PMD structure than the other cell types. PMDs comprise about 50–75% of the genome. b Graphical representation of the relative (percentage) contribution of each state in the 15-state ChromH3M model. Twenty-six percent of the genome shares the same PMDs across all samples and roughly one third differ between them. c Genome-wide normalized histone mark signals within PMDs (including 100 kb flanking regions). Note the enrichment of heterochromatic marks H3K27me3 and H3K9me3 across PMDs and a depletion of the transcription-coupled mark H3K36me3. d Log10-scaled FPKM values of state 10 (Liver-HMDs) associated protein-coding genes. Genes are significantly more highly expressed in hepatocyte samples (PHH) than in macrophages, monocytes, and T cells, according to two-way ANOVA and Tukey HSD post hoc test (see details in the “Methods” section). Only samples marked with star in aare used for simplicity and since they belong to one consortium