Integration of ENCODE Data by Genome-wide SegmentationPanel A shows an illustrative region with the two segmentations methods (ChromHMM and Segway) in a dense view and the combined segmentation expanded to show each state in GM12878, beneath a compressed view of the GENCODE gene annotations. Note that at this level of zoom and genome browser resolution, some segments appear to overlap although they do not. Segmentation classes are named and coloured according to the scheme in Table 3. Beneath the segmentations are shown each of the normalised signals that were used as the input data for the segmentations. Open Chromatin signals from the DNase 1-seq and FAIRE assays are shown in blue, signal from histone modification ChIP-seq in red and TF ChIP-seq signal for Pol II and CTCF in green. The mauve ChIP-seq control signal (“Input control”) at the bottom was also included as an input to the segmentation. Panel B shows the association of selected TF (left) and RNA (right) elements in the combined segmentation states (x-axis) expressed as an observed/expected ratio for each combination of TF or RNA element and segmentation class using the heatmap scale shown in the keybesides each heatmap. Panel C shows the variability of states between cell lines, showing the distribution of occurrences of the state in the 6 cell lines at specific genome locations — from unique to one cell line to ubiquitous in all six cell lines for five states (CTCF, E, T, TSS, and R). Panel D shows the distribution of the level of methylation at individual sites from RRBS analysis in GM12878 across the different states, showing the expecting hypomethylation at TSSs and hypermethylation of genes bodies (T state) and repressed (R) regions.
