Interactive browser for transcription initiation-defined cis-regulatory elements (CREs) identified using PRIME.
Interactive browser for transcription initiation-defined cis-regulatory elements (CREs) identified using PRIME.
Mapping active cis-regulatory elements from transcription initiation events
Hjörleifur Einarsson, Natsuda Navamajiti, Christian Skov Vaagensø, Stefano Pellegrini, Nicolas Alcaraz, Malte Thodberg, Daniel A. Solvie, Wei-Lin Qiu, Maya U. Sheth, Marta Greedy Escudero, Bram Gorissen, Marco Salvatore, Bradley E. Bernstein, Albin Sandelin, Jesse M. Engreitz, Robert Krautz, Robin Andersson
Preprint: bioRxiv doi:10.64898/2026.05.11.724207
The PRIME toolkit was used to identify active cis-regulatory elements (CREs) from CAGE data. FANTOM5 CAGE datasets used in this resource were downloaded from the FANTOM5 data portal, including a curated set of 760 human CAGE libraries from the FANTOM5 project.
Users of FANTOM5-derived data should cite the primary FANTOM5 reference: FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature 507, 462–470 (2014). DOI: 10.1038/nature13182.
New CAGE sequencing data from K562, HepG2, GM12878, A549, and HCT116 cells were preprocessed and mapped using the PRIMEprep pipeline (v0.1.0).
Downstream analyses were performed in R using PRIME (v0.1.0) and in Python using PRIMEmodel (v1.0.0).
All PRIME predictions and signal tracks in K562, GM12878, HepG2, HCT116, A549 cells and FANTOM5 facets are available at Zenodo (doi: 10.5281/zenodo.19712783, v0.2.0).
Download facet statistics (.tsv)
Download individual BED files below. For bulk downloads and CAGE signal tracks (bigWig), please use the Zenodo repository.
This work was supported by grants from the Novo Nordisk Foundation, the Independent Research Fund Denmark, the Lundbeck Foundation, and the Villum Foundation.
For inquiries regarding this work, please contact the PRIME team at the Tissue Gene Regulation Lab and the Andersson Lab.