Published November 16, 2021
| Version v1
Dataset
Open
GREEN-VARAN additional regions resources
Description
Processed functional regions datasets to be used with GREEN-VARAN
This repository contains the GRCh37 and GRCh38 files as indexed BED files. The GRCh38 version of UCNE and TAD were obtained by coordinate liftover.
- TFBS from ENCODE v3
- DNase hypersensitivity peaks from ENCODE v3
- UCNE (ultra-conserved non-coding elements) from https://ccg.epfl.ch/UCNEbase/
- TAD (topologically associating chromatin domains) from http://dna.cs.miami.edu/TADKB/
- Super enhancer from dbSuper at http://bioinfo.au.tsinghua.edu.cn/dbsuper/
Please refer to the original datasets listed in related identifiers and references for eventual limits in use and distribution
Files
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Additional details
Related works
- Is derived from
- Dataset: https://ccg.epfl.ch/UCNEbase/data/download/clusters/hg19_clusters_coord.bed (URL)
- Dataset: http://dna.cs.miami.edu/TADKB/download/TAD_annotations.tar.gz (URL)
- Dataset: https://asntech.org/dbsuper/download_bed_all.php?genome=hg19 (URL)
References
- TADKB paper: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5551-2
- UCNE database paper: https://academic.oup.com/nar/article/41/D1/D101/1057253
- dbSuper paper: https://academic.oup.com/nar/article/44/D1/D164/2502575
- ENCODE paper: https://www.nature.com/articles/s41586-020-2493-4