Name
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 cu-rated 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. |
Year | DOI | Venue |
|---|---|---|
2021 | 10.1093/nar/gkaa943 | NUCLEIC ACIDS RESEARCH |
DocType | Volume | Issue |
Journal | 49 | D1 |
ISSN | Citations | PageRank |
0305-1048 | 0 | 0.34 |
References | Authors | |
0 | 19 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| fan wang | 1 | 34 | 18.08 |
| Xuefeng Bai | 2 | 1 | 1.37 |
| Yue-Zhu Wang | 3 | 0 | 0.68 |
| Yong Jiang | 4 | 1 | 3.06 |
| Bo Ai | 5 | 1 | 1.71 |
| Yin Zhang | 6 | 139 | 18.20 |
| Yuejuan Liu | 7 | 1 | 1.03 |
| Mingcong Xu | 8 | 0 | 0.68 |
| Qiuyu Wang | 9 | 1 | 3.06 |
| Xiaole Han | 10 | 89 | 7.28 |
| Qi Pan | 11 | 1 | 2.38 |
| Yanyu Li | 12 | 0 | 2.37 |
| Xuecang Li | 13 | 1 | 3.06 |
| Jian Zhang | 14 | 71 | 13.59 |
| Jun Zhao | 15 | 16 | 11.09 |
| Guorui Zhang | 16 | 0 | 0.34 |
| Chenchen Feng | 17 | 0 | 1.69 |
| Jiang Zhu | 18 | 0 | 0.68 |
| Chunquan Li | 19 | 4 | 4.46 |