PRIME atlas of transcription initiation-derived gene regulatory elements in human cells

Version 0.2.0 (April 23, 2026):
- Updated all BED files to include UCSC/IGV-compatible coloring (itemRgb)
- Added TPM-normalized CAGE signal tracks for cell lines K562, GM12878, A549, HepG2, HCT116
- Updated README

This resource provides genome-wide maps of transcription initiation-derived cis-regulatory elements (CREs) identified using the PRIME computational framework. The dataset includes cell line-specific predictions, FANTOM5 facet-level predictions, merged facet predictions, pooled CRE datasets, and TPM-normalized CAGE signal tracks.

 

CRE predictions are provided as coordinate-sorted BED files (bgzip-compressed and tabix-indexed) for efficient genomic querying, while strand-specific bigWig files provide genome browser-ready visualization of transcription initiation activity across FANTOM5 facets.

 

The resource contains:

• cell line-specific CRE predictions (tar archived)

• FANTOM5 facet-level CRE predictions (tar archived)

• pooled and merged CRE datasets

• TPM-normalized bigWig signal tracks (tar archived)

 

All files are based on the GRCh38 genome assembly and are directly compatible with tools such as tabix, IGV, and the UCSC Genome Browser.