Encode-enhancers
From GersteinInfo
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(described in papers: [http://www.ncbi.nlm.nih.gov/pubmed/23221638 Hoffman et al, NAR, 2013;] [http://www.ncbi.nlm.nih.gov/pubmed/22426492 Hoffman et al, Nature Methods, 2013;] and [http://www.ncbi.nlm.nih.gov/pubmed/22373907 Ernst and Kellis, Nature Methods, 2012]) | (described in papers: [http://www.ncbi.nlm.nih.gov/pubmed/23221638 Hoffman et al, NAR, 2013;] [http://www.ncbi.nlm.nih.gov/pubmed/22426492 Hoffman et al, Nature Methods, 2013;] and [http://www.ncbi.nlm.nih.gov/pubmed/22373907 Ernst and Kellis, Nature Methods, 2012]) | ||
and | and | ||
| - | http:// | + | http://encodenets.gersteinlab.org/metatracks/ |
(described in [http://papers.gersteinlab.org/papers/metatrack Yip et al, Genome Biol, 2012)]) | (described in [http://papers.gersteinlab.org/papers/metatrack Yip et al, Genome Biol, 2012)]) | ||
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Distal regulatory modules (DRMs) from Yip et al for different cell lines followed by the union in all cell lines: | Distal regulatory modules (DRMs) from Yip et al for different cell lines followed by the union in all cell lines: | ||
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_Gm12878_merged.bed DRM_Gm12878_merged.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_H1hesc_merged.bed DRM_H1hesc_merged.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_Helas3_merged.bed DRM_Helas3_merged.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_Hepg2_merged.bed DRM_Hepg2_merged.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_K562_merged.bed DRM_K562_merged.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_union_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: | Enhancer states extracted from combined ChromHMM/Segway segmentation states in individual cell lines followed by the union in all cell lines: | ||
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.gm12878.enhancer.bed chromhmm_segway.gm12878.enhancer.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.h1hesc.enhancer.bed chromhmm_segway.h1hesc.enhancer.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.helas3.enhancer.bed chromhmm_segway.helas3.enhancer.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.hepg2.enhancer.bed chromhmm_segway.hepg2.enhancer.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.huvec.enhancer.bed chromhmm_segway.huvec.enhancer.bed] |
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.k562.enhancer.bed chromhmm_segway.k562.enhancer.bed] |
| - | [http://archive.gersteinlab.org/proj/Encode_enhancers/ | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.all_celllines.enhancer.bed chromhmm_segway.all_celllines.enhancer.bed ] |
== Unions and Intersections == | == Unions and Intersections == | ||
| Line 46: | Line 46: | ||
Intersection: ChromHMM/Segway enhancers that intersect with DRMs | Intersection: ChromHMM/Segway enhancers that intersect with DRMs | ||
| - | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.drm.intersect.uniq.bed chromhmm_segway.drm.intersect | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.drm.intersect.uniq.bed chromhmm_segway.drm.intersect.bed ] |
Union: Union of all enhancers | Union: Union of all enhancers | ||
| - | [http:// | + | [http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.drm.union.uniq.bed chromhmm_segway.drm.union.bed] |
Latest revision as of 00:26, 25 October 2013
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://encodenets.gersteinlab.org/metatracks/
(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:
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
