ChIPBase v2.0 Home
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Welcome to ChIPBase!


ChIPBase v2.0 is an open database for studying the transcription factor binding sites and motifs, and decoding the transcriptional regulatory networks of lncRNAs, miRNAs, other ncRNAs and protein-coding genes from ChIP-seq data. Our database currently contains ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species.

We develop Co-Expression tool to explore the co-expression patterns between DNA-binding proteins and a variety of genes with ~20,000 RNA-seq gene expression data. We also provide ChIP-Function tool and genome browser to predict functions of diverse genes and visualize various ChIP-seq data.

How to cite:

ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Zhou KR, Liu S, Sun WJ, Zheng LL, Zhou H, Yang JH*, Qu LH*. Nucleic Acids Res. 2017 Jan 04;45(D1):D43-D50. Epub 2016 Oct 23

ChIPBase: A database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Yang JH, Li JH, Jiang S, Zhou H and Qu LH*. Nucleic Acids Res. 2013 Jan;41:D177-87.Epub 2012 Nov 17


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Release notes

Release version 2.3.4 (2016-11-23)
  Improved the performance of Co-Expression tool.
Release version 2.3.3 (2016-09-19)
  Download center is on line now.
Release version 2.3.2 (2016-09-14)
  Improved performance and updated the RNA-seq datasets.
Release version 2.3.0 (2016-08-10)
  Added Co-Experession tool.
  • ~9,900 miRNA-seq and ~10,300 RNA-seq data (32 cancer types) from TCGA project.
  • ~7,800 RNA-seq data (31 normal tissues) from GTEx project.
  • ~1,300 RNA-seq data from EBI Expression Atlas.
Release version 2.2.0 (2016-07-21)
  Updated gene annotation sets of human and mouse.   Added experiment density files to ChIPBase browser.
  • BigWig files: ~1350
Release version 2.1.0 (2016-06-01)
  Finished data import and website development.
  • Species: 10
  • Samples: ~10,200
  • DNA-binding proteins: ~1,290
  • Histone modifications: ~150
  • Technologies: ChIP-seq, ChIP-exo, MNChIP-seq

Sample Statistics in 10 Species

Human           Mouse     Fruitfly   Worm     
A. Thaliana     Yeast      Rat        Zebrafish    
X. tropicalis     Chicken