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, and is closely associated with various biological processes and human diseases. Human ATAC-seq datasets are accumulating rapidly, it is necessary to collect and process these datasets. More importantly, a large number of researches showed that accessible chromatin regions, as well as the related SNPs and TFs, have a strong influence on human diseases and biological processes.
Here, we developed a comprehensive human chromatin accessibility database (ATACdb, http://www.licpathway.net/ATACdb), which aims to provide a large number of available resources on human chromatin accessibility data. ATACdb provides a quality assurance process including four quality control (QC) metrics. ATACdb provides other detailed (epi) genetic annotation information in chromatin accessibility regions, including super-enhancers, typical enhancers, TFs, common SNPs, risk SNPs, eQTLs, LD SNPs, DNA methylation sites, 3D chromatin interactions and TADs. ATACdb provides accurate inference of TF footprint within chromatin accessibility regions. ATACdb is a powerful platform that provides the most comprehensive accessible chromatin data, quality control report, TF footprint and various other annotation information for users.
The current version of ATACdb documented a total of 52,078,883 regions from over 1400 chromatin accessibility ATAC-seq samples. These samples have been manually curated and classified from NCBI GEO/SRA. Accessibile chromatin regions were identified by using a unified system environment and software parameters. ATACdb provides a conveniently user-friendly interface to query, browse, analyze and download accessible chromatin regions and their related annotation information.
For more detailed statistics, please see the "Statistics" page.
|ATACdb database contains 13 columns separated by tab:||Description|
|ATAC-seq||Assay for Transposase Accessible Chromatin with high-throughput sequencing.|
|TF footprint||A measure of TF occupancy, Tn5 footprint for motif sites falling into ATAC-seq data. TF footprint analysis using HINT, which parameters were set as described by Gusmao et al.|
|TC||TC (Tag Count) indicated the number of reads around putative transcription factor binding sites. We used TC to rank footprint prediction.|
|TF protection score||TF protection score was calculated by measuring the different Tn5 digestion numbers between flanking regions and TFBS, which indicated footprints with potential short residence binding times.|
|‘Important’ in the context||To highlight the importance of this information, we added the label "important" on the detail page of accessible chromatin region.|
|Overlap rate||The overlap ratio between a certain sample of accessible chromatin regions and another sample of accessible chromatin regions.|
|Biosample type||Cell type classification of samples.|
|Tissue type||Samples tissue type.|
|Cancer type||Samples cancer type.|
|Biosample name||Biosample name is made of cell/tissue/cell line name, treatment condition, processing time, etc.|
|Start position||The accessible chromatin region is at the start of the chromosome.|
|End position||The accessible chromatin region is at the end of the chromosome.|