Encode-enhancers

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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
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http://papers.gersteinlab.org/papers/metatrack
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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-types:  
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Distal regulatory modules (DRMs) from Yip et al for different cell lines followed by the union in all cell lines:  
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[http://homes.gersteinlab.org/Encode_enhancers/DRM_Gm12878_merged.bed DRM_Gm12878_merged.bed]
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[http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_Gm12878_merged.bed DRM_Gm12878_merged.bed]
   
   
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[http://homes.gersteinlab.org/Encode_enhancers/DRM_H1hesc_merged.bed DRM_H1hesc_merged.bed] <br>
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[http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_H1hesc_merged.bed DRM_H1hesc_merged.bed]  
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[http://homes.gersteinlab.org/Encode_enhancers/DRM_Helas3_merged.bed DRM_Helas3_merged.bed] <br>
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[http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_Helas3_merged.bed DRM_Helas3_merged.bed]
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[http://homes.gersteinlab.org/Encode_enhancers/DRM_Hepg2_merged.bed DRM_Hepg2_merged.bed] <br>
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[http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_Hepg2_merged.bed DRM_Hepg2_merged.bed]
   
   
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[http://homes.gersteinlab.org/Encode_enhancers/DRM_K562_merged.bed DRM_K562_merged.bed] <br>
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[http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_K562_merged.bed DRM_K562_merged.bed]  
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== Unions and Insections ==
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[http://archive.gersteinlab.org/proj/Encode_enhancers/DRM_union_merged.bed DRM_union_merged.bed]
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[http://homes.gersteinlab.org/Encode_enhancers/DRM_union_merged.bed DRM_union_merged.bed]: Union of DRM bins merged into regions, allowing gaps of 1 bin in size <br>
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[http://homes.gersteinlab.org/Encode_enhancers/ENHANCER_CHROMHMM_SEGWAY_DRM.intersect.bed ENHANCER_CHROMHMM_SEGWAY_DRM.intersect.bed]: ChromHMM/Segway enhancers that intersect with DRMs <br>
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[http://homes.gersteinlab.org/Encode_enhancers/ENHANCER_CHROMHMM_SEGWAY_DRM.union.bed ENHANCER_CHROMHMM_SEGWAY_DRM.union.bed]: Union of all enhancers <br>
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Enhancer states extracted from combined ChromHMM/Segway segmentation states in individual cell lines followed by the union in all cell lines:  
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[http://homes.gersteinlab.org/Encode_enhancers/chromhmm.segway.all_celllines.enhancer.sorted.bed chromhmm.segway.all_celllines.enhancer.sorted.bed ] <br>
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[http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.gm12878.enhancer.bed chromhmm_segway.gm12878.enhancer.bed]  
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[http://homes.gersteinlab.org/Encode_enhancers/chromhmm_segway.gm12878.enhancer.bed chromhmm_segway.gm12878.enhancer.bed] <br>
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[http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.h1hesc.enhancer.bed chromhmm_segway.h1hesc.enhancer.bed]  
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[http://homes.gersteinlab.org/Encode_enhancers/chromhmm_segway.h1hesc.enhancer.bed chromhmm_segway.h1hesc.enhancer.bed] <br>
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[http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.helas3.enhancer.bed chromhmm_segway.helas3.enhancer.bed]
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[http://homes.gersteinlab.org/Encode_enhancers/chromhmm_segway.helas3.enhancer.bed chromhmm_segway.helas3.enhancer.bed] <br>
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[http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.hepg2.enhancer.bed chromhmm_segway.hepg2.enhancer.bed]  
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[http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.huvec.enhancer.bed chromhmm_segway.huvec.enhancer.bed]
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[http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.k562.enhancer.bed chromhmm_segway.k562.enhancer.bed]
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[http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.all_celllines.enhancer.bed chromhmm_segway.all_celllines.enhancer.bed ]
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== Unions and Intersections ==
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Intersection: ChromHMM/Segway enhancers that intersect with DRMs
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[http://homes.gersteinlab.org/Encode_enhancers/chromhmm_segway.hepg2.enhancer.bed chromhmm_segway.hepg2.enhancer.bed] <br>
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[http://archive.gersteinlab.org/proj/Encode_enhancers/chromhmm_segway.drm.intersect.uniq.bed chromhmm_segway.drm.intersect.bed ]
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[http://homes.gersteinlab.org/Encode_enhancers/chromhmm_segway.huvec.enhancer.bed chromhmm_segway.huvec.enhancer.bed] <br>
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Union: Union of all enhancers
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[http://homes.gersteinlab.org/Encode_enhancers/chromhmm_segway.k562.enhancer.bed chromhmm_segway.k562.enhancer.bed] <br>
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[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:

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

chromhmm_segway.drm.union.bed

Retrieved from "https://info.gersteinlab.org/Encode-enhancers"
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