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Regulatory Segmentation

Regulatory Segmentation

Segmentations partition the genome into regions such as predicted promoters, enhancers, and repressed (see table below). These are genomic regions of similar signal over a selected number of assays. Each defines a single-track summary of the functional architecture of the human genome in one of six cell types.

Two unsupervised segmentation programs are used to build segmentations:

  • ChromHMM (Ernst et al., 2011)

    ChromHMM labels each assay as high or low in 200 base pair bins over the whole human genome.

  • Segway (Hoffman et al., 2011)

    A Dynamic Bayesian Network approach using base-pair resolution real valued signal data, trained over the ENCODE pilot regions (1% of the genome), and fitted over the whole genome.


Currently there is one set of human segmentations, performed on Segway with a 200bp resolution. The assays were generated in the ENCODE and Roadmap Epigenomic projects for A549, DND-41, GM12878, K562, H1-hESC, HepG2, HeLa-S3, HSSM, HSSMtube, HUVEC, IMR90, Monocytes-CD14+, NH-A, NHDF-AD, NHEK, Nhlf and Osteoblasts, and were chosen to maximise information content about the state of the genome. These assays (including control input sequencing) were coordinated across all cell lines and constituted from three classes of data:

Input Data ClassDescription
Open chromatinDNase1 hypersensitivity
Transcription factorsCTCF
Histone modificationsH3k4me1, H3k4me2, H3k4me3, H3k9ac, H3k27ac, H3k27me3, H3k36me3, H4k20me1

Regulatory Segmentation in the Browser

There is one segmentation track available for each of the cell types in the human Ensembl Regulatory Build. These tracks are on by default in most regulation views, but not in the Location tab. Once in the Location tab, you need to configure the page to turn on the Segmentation tracks as show below.

Selecting segmentation tracks

The colours used for each of the segmentation classes follows the agreed ENCODE standard (a legend is displayed at the bottom of any window displaying regulatory features).