# dbscATAC: a resource of single-cell super-enhancers/enhancers and gene markers derived from scATAC-seq data

## TL;DR

dbscATAC is a database that provides detailed annotations of super-enhancers, enhancers, and gene markers from scATAC-seq data across multiple species and cell types.

## Contribution

dbscATAC introduces a comprehensive, annotated resource of super-enhancers, enhancers, and gene markers derived from scATAC-seq data using improved machine learning.

## Key findings

- Identified 213,835 super-enhancers across 520 tissue/cell types in three species.
- Provided 347,484 gene markers and 10,402,346 enhancer–gene interactions from over 1.6 million single cells.
- Developed an online platform for querying and visualizing single-cell regulatory elements.

## Abstract

scATAC-seq enables high-resolution mapping of cis-regulatory elements. It has been widely applied to uncover cell-type-specific regulatory networks and complement scRNA-seq analysis in numerous studies. However, a large number of datasets generated by scATAC-seq remain underutilized due to limited exploration of super-enhancers/typical enhancers and gene markers. A comprehensive resource enabling cell-type-specific annotation of cis-regulatory elements and their dynamic enhancer–gene linkages remains an urgent unmet need for scATAC-seq.

We present dbscATAC, a specialized single-cell database for annotating super-enhancers, gene markers, and enhancer–gene interactions derived from scATAC-seq data. Using improved machine learning algorithms, we identified 213 835 super-enhancers across 520 tissue/cell types from three species, as well as 347 484 gene markers, 13 470 526 enhancers, and 10 402 346 enhancer–gene interactions derived from 1 668 076 single cells spanning 1028 tissue/cell types in 13 species. An easy-to-use online platform with multiple analytic modules and hierarchical query options was developed for searching, browsing and visualizing single-cell super-enhancers, enhancers, and gene markers. dbscATAC provides a comprehensive resource to facilitate the exploration of enhancer landscapes, gene regulation, and cell-type-specific characteristics in single-cell epigenomics.

The database with all the super-enhancer/enhancer annotation data is available at http://singlecelldb.com/dbscATAC/index.php. And the source code of dbscATAC for prediction of SEs, enhancers, and gene markers are available at https://github.com/EvansGao/dbscATAC. The source code, tissue/cell type description, and data summary can be downloaded at DOI: 10.6084/m9.figshare.28706414.

scATAC-seq, Database, Super-enhancers/enhancers, Gene markers