ATAC-seq and Bisulfite-seq data have been newly added to ChIP-Atlas.
- Database Integration Coordination Program
On October 4, 2021, Associate Professor Shinya Oki of Kyoto University added ATAC-seq and Bisulfite-seq data to "ChIP-Atlas", an epigenomics database supported by JST-NBDC Database Integration Coordination Program (DICP).
By adding ATAC-seq and Bisulfite-seq data to "ChIP-Atlas", users can comprehensively analyze not only information of transcription factors binding to genome and histone modifications, but also of DNA methylations and open chromatin regions. More sophisticated in silico integrated analysis in epigenomics research can be performed easily using new "ChIP-Atlas".
"ChIP-Atlas" is a database that re-analyzes almost all the published data of ChIP-seq, DNase-seq, ATAC-seq and Bisulfite-seq data using unified protocols, respectively, and organizes them by antigens, species and cell types. "ChIP-Atlas" includes the following functions,
- Showing various antigen binding peaks of multiple experiments in a genome browser in parallel.
- Listing up target genes for a specified transcription factor.
- Investigating co-localized transcription factors.
- Predicting transcription factors controlling a given gene set by enrichment analysis.
- ChIP-seq: an experimental method to detect genomic regions to which DNA-binding proteins such as transcription factors are bound, or to detect methylated or acetylated histone regions, by chromatin immunoprecipitation.
- DNase-seq: an experimental method to detect open chromatin regions using DNase I.
- ATAC-seq: an experimental method to detect open chromatin regions using modified Tn5 transposase.
- Bisulfite-seq: an experimental method to detect methylated DNA regions of genome using bisulfite.
Contents of ChIP-Atlas (October 4, 2021)
- ChIP-seq 131,473 experiments
- ATAC-seq 52,135 experiments
- DNA-seq 2,869 experiments
- Bisulfite-seq 28,696 experiments
- Other 9,486 experiments
Total 224,659 experiments
- Funded projects: "Development of an integrative epigenome database"
- ChIP-Atlas | Integbio Database Catalog
Summary of ChIP-Atlas.
- ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data Shinya Oki, Tazro Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, and Chikara Meno EMBO Reports, 2018, e46255.（doi: 10.15252/embr.201846255）