ArticleNucleic acids research2021
ATACdb: a comprehensive human chromatin accessibility database.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed, 74 citations in OpenAlex.
- EnhancerDB 2.0: a comprehensive cross-species enhancer atlas.Molecular biology and evolution · 2026Article
- cfDECOR: a novel approach for estimating cell type contributions to cfDNA based on chromatin accessibility patterns.Scientific reports · 2026Article
- VISDB 2.0: A manually curated resource of viral integration sites and their regulatory maps in human diseases.Scientific data · 2026Article
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- A generic reference defined by consensus peaks for single-cell ATAC-seq data analysis.Nature communications · 2026Article
- ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse.Nucleic acids research · 2026Article
- Mapping Non-Coding Epimutations in Breast Cancer: Advancing Epigenetics Towards Precision Medicine.Sub-cellular biochemistry · 2026Review
- Cross-dataset pan-cancer detection by correlating cell-free DNA fragment coverage with open chromatin sites across cell types.Nature communications · 2025Article
- Article
- Individuals with intellectual disability have an increased burden ofmedRxiv : the preprint server for health sciences · 2025Article
- CanASM: a comprehensive database for genome-wide allele-specific DNA methylation identification and annotation in cancer.BMC genomics · 2025Article
- CASHeart: A database of single cells chromatin accessibility for the human heart.Quantitative biology (Beijing, China) · 2025Article
- HemaCisDB: An Interactive Database for Analyzing Cis-regulatory Elements Across Hematopoietic Malignancies.Genomics, proteomics & bioinformatics · 2025Article
- TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data.Nature communications · 2025Article
- TFTG: A comprehensive database for human transcription factors and their targets.Computational and structural biotechnology journal · 2024Article
- Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data.Cell systems · 2024Article
- DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants.Genome biology · 2024Article
- Super-enhancer omics in stem cell.Molecular cancer · 2024Review
- Proteogenomic network analysis reveals dysregulated mechanisms and potential mediators in Parkinson's disease.Nature communications · 2024Article
- FastBiCmrMLM: a fast and powerful compressed variance component mixed logistic model for big genomic case-control genome-wide association study.Briefings in bioinformatics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.