This page contains information on putative regulatory genomic regions as analyzed within the Roadmap Epigenomics project.
These regulatory regions are annotated using epigenomic information across more than a hundred different cell types.
Although the first version of the HoneyBadger set of regions is being used in the Roadmap epigenomics integrative paper,
the other sets available here have yet to be officially released.
They're being made available here on a collaborative basis and your feedback on their use is greatly appreciated.
Please indicate whether you're using any of these data by filling out this spreadsheet.
Information on the data and samples used:
- The sample spreadsheet maintained by Anshul Kundaje can be found here.
- A graphical summary can be found here.
- Epigenome sample names and associated colors, with order indicated in last column (RData, txt).
HoneyBadger (WM20131211)
Regions delineated using observed DNaseI data across 39 epigenomes,
annotated with the 5-mark 15-state model based on observed data
across 111 Roadmap reference epigenomes.
HoneyBadger2 (WM20140520, to replace HoneyBadger)
Regions delineated using observed DNaseI data across 53 epigenomes,
annotated with the 5-mark 15-state model based on observed data
across 127 epigenomes (Roadmap + ENCODE).
HoneyBadger2-impute (WM20140620, imputation-based HoneyBadger2)
Regions delineated using observed DNaseI data across 53 epigenomes,
annotated with the 12-mark 25-state model based on imputed data
across 127 epigenomes (Roadmap + ENCODE).
HoneyBadger2-intersect (WM20140626, intersection of HoneyBadger2 and HoneyBadger2-impute)
Regions delineated using observed DNaseI data across 53 epigenomes,
annotated with both the 5-mark 15-state (observed) and 12-mark 25-state (imputed) models
across 127 epigenomes (Roadmap + ENCODE).
These regions are then intersected (e.g., only used as enhancer if found to be enhancer in both models).
