Ovcharenko Group Wiki

The definition of enhancer regions used by:

Sanjar

• Select DHS peaks
• Remove Exons and TSS regions
• Select regions with overlaps to H3K27ac and H3K4me1 peaks.
• Extract 400 bp from the center
• Merge resulting regions

Data files: [dcode common]/enhancer_definitions/sanjar/data_files

• Each directory is a Roadmap ID. Under each directory, there is a file "enhancers.bed" from the corresponding tissue.

Info files: [dcode common]/enhancer_definitions/sanjar/info_files

• jul2013.roadmapData.qc.xlsx : Roadmap IDs with extra explanations
• enhancer_regions.png : diagram of the pipeline
• exon_regions.bed : exon regions extracted from RefSeq
• tss_regions.bed : TSS regions extracted from RefSeq

The DHS, H3K27ac and H3K4me1 ChipSeq files are downloaded from here:

http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/narrowPeak