Segway encyclopedia of human regulatory elements and annotation of 164 human cell types
Libbrecht MW, Rodriguez O, Hoffman MM, Bilmes JA, Noble WS. 2016.
A unified encyclopedia of human functional elements through fully automated annotation of 164 human cell types. Biorxiv preprint: http://dx.doi.org/10.1101/086025.
Download the annotations (hg19)
- Cell type-specific annotations: Directory. Each annotation is in gzipped BED format, where the fourth column is the annotation label.
- Encyclopedia: BED format. Encyclopedia segments are a contiguous regions of high conservation-associated activity score, generally between 300-20,000 bp. Columns correspond to: (1) chromosome; (2) start; (3) end; (4) sum of conservation-associated activity score; (5) average base-wise conservation-associated activity score ; (6+) majority label of each cell type in the segment.
- Label-wise conservation-associated activity scores: tab-delimited format.
Position-wise aggregated conservation-associated activity scores:
BED format. Columns correspond to (1) chromosome; (2) start; (3) end; (4) sum of conservation-associated activity scores at the given position.
View the annotations
Conservation-associated activity score plots
Create a conservation-associated activity score plot for a target region (20-100 kb recommended):
- Quiescent: Inactive region.
- ConstitutiveHet: Heterochromatin marking permanently silent regions, characterized by the histone modification H3K9me3.
- FacultativeHet: Heterochromatin marking regions of cell type-specific repression, characterized by the histone modification H3K27me3. Also known as Polycomb-repressed heterochromatin.
- Transcribed: Transcribed genic region.
- Promoter: Regulatory region that occurs directly upstream of transcription start sites.
- Enhancer: Gene-distal regulatory element.
- RegPermissive: Region with weak marks of regulatory activity such as H3K4me1 or DNase hypersensitivity. May or may not directly control gene expression.
- Bivalent: Regulatory element with marks of both activation (such as H3K27ac) and repression (H3K27me3).
- LowConfidance: An annotation label that the interpretation classifier could not confidently assign to one of the above categories.