GREEN: Genomic Regulatory Elements ENcyclopedia¶
Welcome to the house of GREEN-DB and GREEN-VARAN! This documentation describes the resources part of the Genomic Regulatory Elements Encyclopedia
The GREEN project is made by 3 main components:
1. The GREEN-DB collection¶
The collection includes information useful for the annotation of non-coding variants in regulatory regions
- a database (GREEN-DB) containing ~2.4M regulatory regions in the human genome with information on controlled gene(s) and tissue(s) of activity
- pre-processed indexed BED files representing functional genomic signals (TFBS, DNase peaks, UCNE, TADs)
- pre-processed indexed tables for 12 non-coding variant impact prediction scores and PhyloP100 conservation
The GREEN-DB files can be downloaded from Zenodo: https://zenodo.org/record/5636209 All the additional pre-preprocessed datasets are also available from Zenodo, see the Download section.
2. The GREEN-VARAN tool set¶
This include tools and workflows that can be used to interact with information in the GREEN-DB and annotate VCF files
- annotate small variants or structural variants with regulatory impact information, including possibly controlled genes
- add additional annotations on functional elements and non-coding prediction scores
- prioritize small variants for possible regulatory impact
- given a list of variants or regions, query the GREEN-DB for detailed information
Available from GitHub: https://github.com/edg1983/GREEN-VARAN
3. The prioritization workflow¶
A Nextflow workflow is available to automate download of the GREEN-DB and supporting resources and run the prioritization workflow on a VCF file. This workflow can be run on one or multiple VCF file(s) and will automatically annotated the desired scores and regions and then perform GREEN-VARAN annotation.
How to cite¶
If you find GREEN-DB and GREEN-VARAN useful for your research please cite our manuscript (https://academic.oup.com/nar/article/50/5/2522/6541021) See also the how to cite section
The Download section lists locations to download the GREEN-DB and other resource files for annotation