Paper on ChIP-Atlas published in Nucleic Acids Research. With new advanced analysis functions, it become the infrastructure for epigenomic information with the largest amount of data in the world.

Prof. Shinya Oki of Institute of Resource Development and Analysis, Kumamoto University, and his colleagues published a paper on the major update of ChIP-Atlas on May 16, 2024 in the Web Server Issue of the scientific journal "Nucleic Acids Research". In addition, Kumamoto University and Chiba University issued a press release on this topic on the same day.

ChIP-Atlas is an integrated database of epigenomics. It contains genome-protein interactions (ChIP-seq), open chromatin information (DNase-seq, ATAC-seq), and methylome information (Bisulfite-seq) for human and five model organisms (mouse, rat, Drosophila, nematode, and budding yeast). The major update (ChIP-Atlas 3.0) discussed in this paper was implemented in October 2023. It integrates annotated information such as the three-dimensional structure of the genome (Hi-C) and genomic variation for disease susceptibility, and adds Diff Analysis, a comparative analysis tool that detects changes in epigenomic states related to gene expression regulation

According to the press release, in the six years since its release in 2018, ChIP-Atlas has been cited in nearly 1,000 papers, primarily in the life and medical sciences. Through this major update, ChIP-Atlas has become the infrastructure for epigenomic information with the largest number of data in the world and equipped with advanced analysis capabilities. It is expected to further contribute to the elucidation of pathogenic mechanisms of genetic diseases and drug action mechanisms, as well as to the efficiency of research on cellular differentiation and transformation.

ChIP Atlas is being developed as part of the JST Program for Database Integration Coordination Program (DICP), "Construction of an integrative data platform for transcriptional regulations (Principal Investigator: KASUKAWA Takeya, Team Leader, Center for Integrative Medical Sciences, Riken".
For more information, see the paper and the press release.

Data in ChIP-Atlas Data (ChIP-Atlas Version 3)

• ChIP-seq (genome-protein interactions) 228,495 entries
• ATAC-seq (open chromatin information) 84,615 entries
• DNase-seq (open chromatin information) 6,386 entries
• Bisulfite-seq (methylome information) 56,668 entries
• Total 376,164 entries