is a Data Source.
ChIP-Atlas is a data-mining suite that integrates and uniformly reprocesses nearly all public ChIP-seq, ATAC-seq, DNase-seq and Bisulfite-seq experiments deposited in the Sequence Read Archive for six model organisms (human, mouse, rat, fruit fly, nematode and budding yeast). It provides peak calls, coverage tracks, target gene predictions, colocalization analyses, enrichment analysis, differential analysis and, since version 3.0, chromosome architecture data, with manually curated antigen and cell type annotations.
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| chip-atlas.portal | ChIP-Atlas Web Portal | chip-atlas.org | Graphical Interface | http | ChIP-Atlas web portal with the Peak B... |
| chip-atlas.experimentlist | ChIP-Atlas experimentList.tab | experimentList.tab (342.8 MB) | Product | tsv | Metadata table describing every ChIP-... |
| chip-atlas.filelist | ChIP-Atlas fileList.tab | fileList.tab (121.0 MB) | Product | tsv | Table listing the assembled peak-call... |
| chip-atlas.peaks.each | ChIP-Atlas Per-Experiment Peak Calls and Coverage | data | Product | mixed | Peak calls (MACS2, BED4 and BigBed) a... |
| chip-atlas.peaks.assembled | ChIP-Atlas Assembled Peak-call Data | Oth.ALL.05.GATA2.AllCell.bed (607.9 MB) | Product | txt | Assembled BED9 peak-call files used i... |
| chip-atlas.peaks.light | ChIP-Atlas All Peaks (Light) | allPeaks_light.hg38.05.bed.gz (19.9 GB) | Product | txt | Lighter version of all peak-call data... |
| chip-atlas.targetgenes | ChIP-Atlas Target Genes | POU5F1.5.tsv (2.5 MB) | Product | tsv | Predicted target genes of each transc... |
| chip-atlas.colocalization | ChIP-Atlas Colocalization | POU5F1.Pluripotent_stem_cell.tsv (264.1 KB) | Product | tsv | Colocalization scores between pairs o... |
| chip-atlas.api | ChIP-Atlas Analysis API | Perform-Enrichment-Analysis-programmatically | Programming Interface | http | Programmatic access to ChIP-Atlas Enr... |
| chip-atlas.docs | ChIP-Atlas Documentation | wiki | Documentation | http | ChIP-Atlas documentation covering dat... |
ChIP-Atlas is a data-mining suite for public epigenomic and regulome data. It selects ChIP-seq, ATAC-seq, DNase-seq and Bisulfite-seq experiments from the Sequence Read Archive (SRX, DRX and ERX accessions) for human, mouse, rat, Drosophila melanogaster, Caenorhabditis elegans and Saccharomyces cerevisiae, and reprocesses them with a uniform pipeline (Bowtie2 alignment, MACS2 peak calling at three significance thresholds, BigWig coverage). Curators annotate the antigen and cell type of each experiment, using standard gene nomenclatures (HGNC, MGI, RGD, FlyBase, WormBase, SGD) and unified cell line names.
The web portal offers a Peak Browser (via IGV), Target Genes, Colocalization, Enrichment Analysis and Diff Analysis. ChIP-Atlas 3.0 added chromosome architecture data. It is developed by Shinya Oki, Zhaonan Zou and colleagues with the Database Center for Life Science (DBCLS); the current contacts are at Kumamoto University, and processing runs on the NIG Supercomputer.
Files are served from https://chip-atlas.dbcls.jp/data/, with paths documented on the project wiki. Metadata tables (experimentList.tab, fileList.tab, analysisList.tab, antigenList.tab, celltypeList.tab) are under data/metadata/. Per-experiment BED, BigBed and BigWig files, assembled Peak Browser BED files, gzipped “light” peak sets, and Target Genes and Colocalization TSV tables sit in per-genome directories (for example data/hg38/).
The portal says all ChIP-Atlas data and analysis tools are licensed under CC BY 4.0, with attribution to the ChIP-Atlas publications. The website source code on GitHub is MIT licensed. An older snapshot in the NBDC Life Science Database Archive (doi:10.18908/lsdba.nbdc01558-000) is listed there as CC BY-SA.
Created: October 05, 2026 | Last modified: October 05, 2026