ATACdb: a comprehensive human chromatin accessibility database. Issue Volume 49:Issue D1(2021) (30th October 2020)

• Record Type: Journal Article
• Authors: Wang, Fan; Bai, Xuefeng; Wang, Yuezhu; Jiang, Yong; Ai, Bo; Zhang, Yong; Liu, Yuejuan; Xu, Mingcong; Wang, Qiuyu; Han, Xiaole; Pan, Qi; Li, Yanyu; Li, Xuecang; Zhang, Jian; Zhao, Jun; Zhang, Guorui; Feng, Chenchen; Zhu, Jiang; Li, Chunquan
• Is Part Of: Nucleic acids research. Volume 49:Issue D1(2021)
• Page Start: D55
• Page End: D64
• Publication Date: 2020-10-30
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa943
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Accessible chromatin is a highly informative structural feature for identifying regulatory elements, which provides a large amount of information about transcriptional activity and gene regulatory mechanisms. Human ATAC-seq datasets are accumulating rapidly, prompting an urgent need to comprehensively collect and effectively process these data. We developed a comprehensive human chromatin accessibility database (ATACdb, http://www.licpathway.net/ATACdb ), with the aim of providing a large amount of publicly available resources on human chromatin accessibility data, and to annotate and illustrate potential roles in a tissue/cell type-specific manner. The current version of ATACdb documented a total of 52 078 883 regions from over 1400 ATAC-seq samples. These samples have been manually curated from over 2200 chromatin accessibility samples from NCBI GEO/SRA. To make these datasets more accessible to the research community, ATACdb provides a quality assurance process including four quality control (QC) metrics. ATACdb provides detailed (epi)genetic annotations in chromatin accessibility regions, including super-enhancers, typical enhancers, transcription factors (TFs), common single-nucleotide polymorphisms (SNPs), risk SNPs, eQTLs, LD SNPs, methylations, chromatin interactions and TADs. Especially, ATACdb provides accurate inference of TF footprints within chromatin accessibility regions. ATACdb is a powerful platform that provides the most comprehensive accessible chromatin data, QC, TF footprint and various other annotations.