Encode-enhancers
From GersteinInfo
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| - | Distal regulatory modules (DRMs) from Yip et al for different cell | + | Distal regulatory modules (DRMs) from Yip et al for different cell lines followed by the union in all cell lines: |
[http://homes.gersteinlab.org/Encode_enhancers/DRM_Gm12878_merged.bed DRM_Gm12878_merged.bed] | [http://homes.gersteinlab.org/Encode_enhancers/DRM_Gm12878_merged.bed DRM_Gm12878_merged.bed] | ||
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[http://homes.gersteinlab.org/Encode_enhancers/DRM_union_merged.bed DRM_union_merged.bed] | [http://homes.gersteinlab.org/Encode_enhancers/DRM_union_merged.bed DRM_union_merged.bed] | ||
| - | Enhancer states extracted from combined ChromHMM/Segway | + | 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.gm12878.enhancer.bed chromhmm_segway.gm12878.enhancer.bed] | [http://homes.gersteinlab.org/Encode_enhancers/chromhmm_segway.gm12878.enhancer.bed chromhmm_segway.gm12878.enhancer.bed] | ||
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[http://homes.gersteinlab.org/Encode_enhancers/chromhmm_segway.k562.enhancer.bed chromhmm_segway.k562.enhancer.bed] | [http://homes.gersteinlab.org/Encode_enhancers/chromhmm_segway.k562.enhancer.bed chromhmm_segway.k562.enhancer.bed] | ||
| + | [http://homes.gersteinlab.org/Encode_enhancers/chromhmm.segway.all_celllines.enhancer.sorted.bed chromhmm.segway.all_celllines.enhancer.sorted.bed ] | ||
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| - | [http://homes.gersteinlab.org/Encode_enhancers/ENHANCER_CHROMHMM_SEGWAY_DRM. | + | == Unions and Intersections == |
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| + | Intersection: ChromHMM/Segway enhancers that intersect with DRMs | ||
| + | [http://homes.gersteinlab.org/Encode_enhancers/ENHANCER_CHROMHMM_SEGWAY_DRM.intersect.bed ENHANCER_CHROMHMM_SEGWAY_DRM.intersect.bed] | ||
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| + | Union: Union of all enhancers | ||
| + | [http://homes.gersteinlab.org/Encode_enhancers/ENHANCER_CHROMHMM_SEGWAY_DRM.union.bed ENHANCER_CHROMHMM_SEGWAY_DRM.union.bed] | ||
Revision as of 20:21, 27 September 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://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:
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.sorted.bed
Unions and Intersections
Intersection: ChromHMM/Segway enhancers that intersect with DRMs ENHANCER_CHROMHMM_SEGWAY_DRM.intersect.bed
Union: Union of all enhancers ENHANCER_CHROMHMM_SEGWAY_DRM.union.bed
