Encode-enhancers

From GersteinInfo

This page lists the ENCODE 2 enhancers

These files are derived from data at http://www.ebi.ac.uk/~swilder/Superclustering/concordances4 (described in papers: Hoffman et al, NAR, 2013; Hoffman et al, Nature Methods, 2013; and Ernst and Kellis, Nature Methods, 2012) and http://papers.gersteinlab.org/papers/metatrack (described in Yip et al, Genome Biol, 2012))

Original Data Files

Distal regulatory modules (DRMs) from Yip et al for different cell lines followed by the union in all cell lines:

DRM_Gm12878_merged.bed

DRM_H1hesc_merged.bed

DRM_Helas3_merged.bed

DRM_Hepg2_merged.bed

DRM_K562_merged.bed

DRM_union_merged.bed

Enhancer states extracted from combined ChromHMM/Segway segmentation states in individual cell lines followed by the union in all cell lines:

chromhmm_segway.gm12878.enhancer.bed

chromhmm_segway.h1hesc.enhancer.bed

chromhmm_segway.helas3.enhancer.bed

chromhmm_segway.hepg2.enhancer.bed

chromhmm_segway.huvec.enhancer.bed

chromhmm_segway.k562.enhancer.bed

chromhmm.segway.all_celllines.enhancer.bed

Unions and Intersections

Intersection: ChromHMM/Segway enhancers that intersect with DRMs

chromhmm_segway.drm.intersect.bed

Union: Union of all enhancers

ENHANCER_CHROMHMM_SEGWAY_DRM.union.bed