ChIPBase v2.0: Decoding Transcriptional Regulactory Networks of Non-coding RNAs and Protein-coding Genes from ChIP-seq Data

ChIPBase v2.0 Home

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 to predict functions of diverse genes.

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.

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

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.

Human: GENCODE v25
Mouse: GENCODE M10

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

Species	Gnome build	Genome sequence	Genome annotation
Human	hg38	UCSC	GENCODE Release 25, miRbase v21
Human	hg19	UCSC	GENCODE Release 25 (mapped to GRCh37), miRbase v20
Mouse	mm10	UCSC	GENCODE Release M10, miRbase v21
Rat	rn6	UCSC	Ensembl Release 84 (Rnor_6.0), miRbase v21 (rn5 converted to rn6 by liftOver)
Chicken	galGal4	UCSC	Ensembl Release 84 (Galgal4), miRbase v21, deepBase v2.0
Zebrafish	danRer10	UCSC	Ensembl Release 84 (GRCz10), miRbase v21(danRer7 converted to danRer10 by liftOver)
X.tropicalis	xenTro3	UCSC	Ensembl Release 84 (JGI_4.2), miRbase v21, deepBase v2.0
Worm	ce11	UCSC	Ensembl Release 84 (WBcel235), miRbase v21
Worm	ce10	UCSC	Ensembl Release 66 (WS220), miRbase v20, deepBase v2.0
Fruitfly	dm6	UCSC	Ensembl Release 84 (BDGP6), miRbase v21 (dm3 converted to dm6 by liftOver)
A.thaliana	TAIR10	Ensembl Plants	Ensembl Release 31 (TAIR10), miRbase v21
Yeast	sacCer3	UCSC	Ensembl Release 84 (R64-1-1)

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