Reprocessed transcribed enhancers in hg38 (GRCh38)

Dalby, Maria; Rennie, Sarah; Andersson, Robin
The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark

= Overview

Transcribed enhancers were identified and their expression was quantified across all human FANTOM5 libraries, following the re-aligned FANTOM5 CAGE data upon hg38 (GRCh38) (obtained from http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v1/basic/), and decomposition-based peak identification (obtained from https://zenodo.org/record/545682#.WPuNy1Pyv2Q) by Kawaji, Hideya.

= Data files

Each predicted enhancer is described in BED12 format with two blocks denoting the merged regions of transcription initiation on the minus and plus strands. The thickStart and thickEnd columns denote the inferred mid position between blocks of transcription initiation events. Expression and usage matrices are tab delimited and the first row gives the FANTOM5 CNhs IDs and the first column the enhancer ID (same as column 4 in BED file). Usage matrices contain zeroes and ones (0:not used, 1:used).

* enhancers (BED12 format)
* enhancer expression matrix (tab delimited, first row: CNhs IDs, first column: enhancer ID (coordinate))
* enhancer expression matrix TPM normalized (tab delimited, first row: CNhs IDs, first column: enhancer ID (coordinate))
* binary enhancer usage matrix (0:not used, 1:used, tab delimited, first row: CNhs IDs, first column: enhancer ID (coordinate))


= Reference/Data citation

The referene of the human enhancer dataset is:
	https://doi.org/10.5281/zenodo.556775

Please use the above URL for data citations like:
	Maria Dalby, Sarah Rennie, & Robin Andersson. (2017). FANTOM5 transcribed enhancers in hg38 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.556775