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

Nucleic Acids Res. 2026 Jan 6;54(D1):D55-D65. doi: 10.1093/nar/gkaf1222.

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.

PMID:41243977 | PMC:PMC12807738 | DOI:10.1093/nar/gkaf1222