#Overview of files associated with "A study of the enhancer-gene interaction architecture: linking enhancer pleiotropy to gene expression breadth in the human genome" (Singh and Yi 2020)
#------------------------------- 1.enhancer_dataset_state15.bed
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BED format file containing all merged and processed genomic coordinates (Hg19) for enhancers identified by chromatin state state 6 (genic enhancers) and state 7 (enhancers)
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Fields (tab-separated): [1]chromosome [2]start [3]stop [4]enhancer index [5]length (bp) [6]enhancer pleiotrophy category [7]number of tissues [8]list of tissues
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Unprocessed files were obtained from the NIH Roadmap Epigenomics Mapping Consortium (http://www.roadmapepigenomics.org/) List of Epigenomes with Roadmap EID E008_ESC ESC E015_ESC ESC E034_BLOOD Blood E050_BLOOD Blood E059_SKIN Skin E063_FAT Fat E066_LIVER Liver E071_BRAIN Brain E073_BRAIN Brain E075_GI_COLON Colon E076_GI_COLON Colon E078_GI_DUODENUM Duodenum E079_GI_ESOPHAGUS Esophagus E080_ADRENAL Adrenal E081_BRAIN Brain E082_BRAIN Brain E083_HEART Heart E084_GI_INTESTINE Intestine E085_GI_INTESTINE Intestine E086_KIDNEY Kidney E087_PANCREAS Pancreas E088_LUNG Lung E089_MUSCLE Muscle E090_MUSCLE Muscle E091_PLACENTA Placenta E092_GI_STOMACH Stomach E093_THYMUS Thymus E094_GI_STOMACH Stomach E095_HEART Heart E096_LUNG Lung E097_OVARY Ovary E098_PANCREAS Pancreas E099_PLACENTA Placenta E101_GI_RECTUM Rectum E103_GI_RECTUM Rectum E108_MUSCLE Muscle E109_GI_INTESTINE Intestine E111_GI_STOMACH Stomach E112_THYMUS Thymus E113_SPLEEN Spleen E126_SKIN Skin E128_LUNG Lung E129_BONE Bone
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Enhancer merging protocol: The union of all enhancers across all samples was taken and outlier regions with the top 5% length (length > 3,500 bp) were removed. Any enhancer regions which overlapped more than 50% were merged.
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