Evidence map›Paper›PMID 41243977›Full record

ArticleNucleic acids research2026

ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse.

Qiao-Li Fang, Feng-Cui Qian, Zheng-Min Yu, Bing-Long Li, Xiang-Yang Meng, Ting Cui, Ting-Ting Yu, Yan-Yu Li, Li-Dong Li, Chen-Chen Feng and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Qiao-Li FangThe First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Feng-Cui QianThe First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Zheng-Min YuSchool of Computer, University of South China, Hengyang, Hunan 421001, China.ORCID 0009-0006-0777-4043
Bing-Long LiInstitute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, China.
Xiang-Yang MengSchool of Computer, University of South China, Hengyang, Hunan 421001, China.
Ting CuiThe First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Ting-Ting YuSchool of Computer, University of South China, Hengyang, Hunan 421001, China.
Yan-Yu LiThe First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Li-Dong LiThe First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
Chen-Chen FengSchool of Computer, University of South China, Hengyang, Hunan 421001, China.
Zi-Rui XiongSchool of Computer, University of South China, Hengyang, Hunan 421001, China.
Qing XunInstitute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan 421001, China.
Chun-Quan LiThe First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.ORCID 0000-0002-4700-5496
Qiu-Yu WangThe First Affiliated Hospital & Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.

Funding

Education Department of Hunan Province 24B0417Innovation Platform and Talent Program 2023TP1047National Natural Science Foundation of China 62171166National Natural Science Foundation of China 62272212National Natural Science Foundation of China 62301246National Natural Science Foundation of China 62572223The Natural Science Foundation of Hunan Province 2025JJ50105The Natural Science Foundation of Hunan Province 2025JJ50401The Science and Technology Innovation Talent Program of Hunan Province of China 2024RC1062University of South China 20224310NHYCG05
6 · The paper itself

Abstract

Chromatin accessibility, which reflects transcriptional activity, is crucial for elucidating gene regulation, cellular function, and disease mechanisms. To provide a more comprehensive chromatin accessibility resource, we have released ATACdb 2.0 (https://www.licpathway.net/ATACdb/), which provides multiple significant improvements over ATACdb 1.0: (i) Substantially expands the data scale by adding new mouse data and expanding human samples, while constructing pseudo-bulk ATAC-seq profiles based on scATAC-seq data to enrich cell type diversity. The current version contains 319 968 559 chromatin accessibility regions (CARs) from 4 031 human samples and 75 639 252 CARs from 1273 mouse samples. Compared with version 1.0, the numbers of samples and regions have increased by 3.5- and 7.5-fold, respectively. (ii) Provides richer genetic and epigenetic regulatory annotations, including silencer regions, CpG islands, meQTLs, histone modifications, eRNAs, transcription co-factors (TcoFs) and transcription factors (TFs), etc. (iii) Adds practical and convenient search and analysis functions, including "Search by SNP", "Genomic regions enrichment analysis", and "Gene-CARs overlapping analysis". (iv) Optimized target gene identification methods and added enrichment analysis of target genes. (v) Provides two additional data quality control metrics. In summary, ATACdb 2.0 provides more comprehensive and reliable resources along with more convenient and flexible functionalities, facilitating the exploration of the role of chromatin accessibility in gene regulation.

Indexed as

ChromatinDatabases, GeneticAnimalsChromatin Immunoprecipitation SequencingCpG IslandsEpigenesis, GeneticHumansMiceMolecular Sequence AnnotationSoftwareTranscription FactorsChromatinTranscription Factors

Identifiers

PMID41243977
PMCPMC12807738

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

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.