ChIP-Atlas is a database collecting the bed files calculated from the ChIP-Seq, DNase-Seq, ATAC-Seq, and Bisulfite-seq data archived in Sequence Read Archive (SRA). The database has a web interface to explore the analysis results from the calculated peak call data. This repository contains the webapp code and the documentation of the database.
ChIP-Atlas is providing online analysis function on ChIP-Atlas - Enrichment Analysis and Diff Analysis. The background calculation relies on the NIG supercomputer system, hosted by DNA Data Bank of Japan, National Institute of Genetics, while the webapp is hosted on its own cloud instance. Therefore, Enrichment Analysis may go down during the maintenance of the NIG supercomputer system. We announce when the function goes down, but if you encountered any trouble other than that period, please inform us from the issue page.
Processed data including the peak-call data in bed, bigBed or bigWig format is available to download via web application interface (example). We also provide the bulk download via LSDB Archive maintained by the National Bioscience Database Center. We provide individual bed/wig data for each experiment and data assembled by the curated metadata. See more details in Wiki.
- Added Annotation tracks to Peak Browser, together with UI improvement (2023/10/25)
- Launched Diff Analysis tool enabling to detect differential peaks or differentially methylated regions (2023/10/25)
- New publication on the NAR web server issue! https://doi.org/10.1093/nar/gkac199 (2022/03/24)
- Minor bug fix: Peak Browser / Enrichment Analysis UI updates the number of experiments by selecting experiment type (2022/03/01)
- Updated the order of the genome assembly tabs, now GRCh38 is default. And some minor fixes came together! (2022/02/08)
- Added ATAC-Seq and Bisulfite-Seq , together with UI improvement including 'peak' icon! (2021/10/04)
- Updated site design: (2021/01/04)
- Dataset search is available as a standalone function
- ID search at the top right corner now accepts GEO Sample ID (e.g. GSM469863) along with SRA Experiment ID (e.g. SRX018625)
- New information layout for individual experiment list
- Added new genome assemblies: hg38, mm10, dm6, ce11. Happy holidays! (2020/12/01)
- Publication on EMBO reports! Oki S, Ohta T, Shioi G, Hatanaka H, Ogasawara O, Okuda Y, Kawaji H, Nakaki R, Sese J, Meno C. ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data. Vol. 19, EMBO reports. EMBO; 2018. http:https://dx.doi.org/10.15252/embr.201846255 (2018/11/09)
- Launched the ChIP-Atlas website! (2015/04/13)
The web server records the queries just for solving issues such as server error. We will not open or distribute those information without an announcement to the users.
- Publication
- Zou Z, Ohta T, Oki S. ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data. Nucleic Acids Research. Oxford University Press (OUP); 2024. https://doi.org/10.1093/nar/gkae358
- Zou Z, Ohta T, Miura F, Oki S. ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data. Nucleic Acids Research. Oxford University Press (OUP); 2022. http:https://dx.doi.org/10.1093/nar/gkac199
- Oki S, Ohta T, Shioi G, Hatanaka H, Ogasawara O, Okuda Y, Kawaji H, Nakaki R, Sese J, Meno C. ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data. Vol. 19, EMBO reports. EMBO; 2018. http:https://dx.doi.org/10.15252/embr.201846255
- Website
- Oki, S; Ohta, T (2015): ChIP-Atlas. http:https://chip-atlas.org
- Database
- Oki, S; Ohta, T (2015): ChIP-Atlas. http:https://dx.doi.org/10.18908/lsdba.nbdc01558-000
- Shinya Oki, Kyoto University
- Metadata curation
- Workflow management and execution
- Zhaonan Zou, Kyoto University
- Data process
- Development of the Diff Analysis tool
- Tazro Ohta, Database Center for Life Science (DBCLS)
- Development/Maintenance of web application
- Development of data model
- Osamu Ogasawara, DNA Data Bank of Japan (DDBJ)
- Support enrichment analysis implementation over NIG supercomputer system
- Hideki Hatanaka, National Bioscience Database Center (NBDC)
- Support data archive on LSDB Archive
See LICENSE.txt for details of copyright of code provided under this repository. Copyright for the data can be browsed at the LSDB Archive website here.