ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data

EMBO Rep. 2018 Dec;19(12):e46255. doi: 10.15252/embr.201846255. Epub 2018 Nov 9.


We have fully integrated public chromatin chromatin immunoprecipitation sequencing (ChIP-seq) and DNase-seq data (n > 70,000) derived from six representative model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast), and have devised a data-mining platform-designated ChIP-Atlas ( ChIP-Atlas is able to show alignment and peak-call results for all public ChIP-seq and DNase-seq data archived in the NCBI Sequence Read Archive (SRA), which encompasses data derived from GEO, ArrayExpress, DDBJ, ENCODE, Roadmap Epigenomics, and the scientific literature. All peak-call data are integrated to visualize multiple histone modifications and binding sites of transcriptional regulators (TRs) at given genomic loci. The integrated data can be further analyzed to show TR-gene and TR-TR interactions, as well as to examine enrichment of protein binding for given multiple genomic coordinates or gene names. ChIP-Atlas is superior to other platforms in terms of data number and functionality for data mining across thousands of ChIP-seq experiments, and it provides insight into gene regulatory networks and epigenetic mechanisms.

Keywords: ChIP‐seq; DNase‐seq; data mining; enhancer; transcription factor.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin Immunoprecipitation*
  • Data Mining*
  • Enhancer Elements, Genetic / genetics
  • Genetic Loci
  • Humans
  • Internet
  • Sequence Analysis, DNA*
  • Transcription Factors / metabolism


  • Transcription Factors