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Welcome to ChIPBase v3.0 !

ChIPBase v3.0 identified ~151,187,000 regulatory relationships between ~171,600 genes and ~3,000 regulators by analyzing ~55,000 ChIP-seq datasets, which represent a 30-fold expansion. Moreover, we de novo identified ~29,000 motif matrices of transcription factors. In addition, we constructed a novel “Enhancer” module to predict ~1,837,200 regulation regions functioning as poised, active or super enhancers under ~1300 conditions. Importantly, we constructed exhaustive coexpression maps between regulators and their target genes by integrating expression profiles of ∼65,000 normal and ∼15,000 tumor samples. We built a “Disease” module to obtain an atlas of the disease-associated variations in the regulation regions of genes. We also constructed an “EpiInter” module to explore potential interactions between epitranscriptome and epigenome. Finally, we designed “Network” module to provide extensive and gene-centred regulatory networks.

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How to cite:

[1] Huang J, Zheng W, Zhang P, Lin Q, Chen Z, Xuan J, Liu C, Wu D, Huang Q, Zheng L, Liu S, Zhou K, Qu L, Li B, Yang J. (2022) ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes. Nucleic Acids Res, 2022 Nov 18:gkac1067.

[2] Zhou, K.R., Liu, S., Sun, W.J., Zheng, L.L., Zhou, H., Yang, J.H. and Qu, L.H. (2017) ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res, 45, D43-D50.

[3] Yang, J.H., Li, J.H., Jiang, S., Zhou, H. and Qu, L.H. (2013) ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res, 41, D177-187.


Thanks to CistromeDB, ReMap2022, ENCODE for providing ChIP-seq peak data.

Thanks to ENCODE, TCGA, GTEx, CCLE, ICGC for providing RNA-seq data.

Thanks to ICGC, COSMIC for providing SNV data.

Thanks to COSMIC, GWAS Catalog for providing SNP data.

Thanks to Ensembl, GENCODE, NCBI RefSeq for providing gene annotation data.


We clear about which data is used form the abovementioned databases and ensure that we have the right to share, adapt, and redistribute the data we have imported.


[1] Zheng, R., Wan, C., Mei, S., Qin, Q., Wu, Q., Sun, H., Chen, C.-H., Brown, M., Zhang, X., Meyer, C.A. et al. (2019) Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res., 47, D729-D735.

[2] Hammal, F., de Langen, P., Bergon, A., Lopez, F. and Ballester, B. (2022) ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. Nucleic Acids Res., 50, D316-D325.

[3] Luo, Y., Hitz, B.C., Gabdank, I., Hilton, J.A., Kagda, M.S., Lam, B., Myers, Z., Sud, P., Jou, J., Lin, K. et al. (2020) New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res., 48, D882-D889.

[4] Cancer Genome Atlas Research, N., Weinstein, J.N., Collisson, E.A., Mills, G.B., Shaw, K.R., Ozenberger, B.A., Ellrott, K., Shmulevich, I., Sander, C. and Stuart, J.M. (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet, 45, 1113-1120.

[5] Lonsdale, J., Thomas, J., Salvatore, M., Phillips, R., Lo, E., Shad, S., Hasz, R., Walters, G., Garcia, F., Young, N. et al. (2013) The Genotype-Tissue Expression (GTEx) project. Nature Genetics, 45, 580-585.

[6] Ghandi, M., Huang, F.W., Jané-Valbuena, J., Kryukov, G.V., Lo, C.C., McDonald, E.R., Barretina, J., Gelfand, E.T., Bielski, C.M., Li, H. et al. (2019) Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature, 569, 503-508.

[7] International Cancer Genome, C., Hudson, T.J., Anderson, W., Artez, A., Barker, A.D., Bell, C., Bernabe, R.R., Bhan, M.K., Calvo, F., Eerola, I. et al. (2010) International network of cancer genome projects. Nature, 464, 993-998.

[8] Tate, J.G., Bamford, S., Jubb, H.C., Sondka, Z., Beare, D.M., Bindal, N., Boutselakis, H., Cole, C.G., Creatore, C., Dawson, E. et al. (2019) COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res, 47, D941-d947.

[9] Buniello, A., MacArthur, J.A.L., Cerezo, M., Harris, L.W., Hayhurst, J., Malangone, C., McMahon, A., Morales, J., Mountjoy, E., Sollis, E. et al. (2019) The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res, 47, D1005-D1012.

[10] Cunningham, F., Allen, J.E., Allen, J., Alvarez-Jarreta, J., Amode, M.R., Armean, I.M., Austine-Orimoloye, O., Azov, A.G., Barnes, I., Bennett, R. et al. (2022) Ensembl 2022. Nucleic Acids Res, 50, D988-D995.

[11] Frankish, A., Diekhans, M., Jungreis, I., Lagarde, J., Loveland, J.E., Mudge, J.M., Sisu, C., Wright, J.C., Armstrong, J., Barnes, I. et al. (2021) GENCODE 2021. Nucleic Acids Res, Nucleic Acids Res, 49, D916-D923.

[12] Pruitt, K.D., Brown, G.R., Hiatt, S.M., Thibaud-Nissen, F., Astashyn, A., Ermolaeva, O., Farrell, C.M., Hart, J., Landrum, M.J., McGarvey, K.M. et al. (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res, 42, D756-763.

Release notes

Current version:
Release version 3.0.0 (2022-09-01)
  Updated ~55,000 ChIP-seq data from ENCODE, CistromeDB, ReMap.
  Updated ~80,000 expression data from ENCODE, TCGA, GTEx, CCLE, ICGC.
  Updated genome (human) to GRCh38.
  Updated genome (mouse) to GRCm39.
  Updated annotation (human) to Release 41.
  Updated annotation (mouse) to Release M30.
  Constructed novel module "Disease".
  Included ~3,993,000 SNP sites from GWAS and COSMIC.
  Included ~88,939,000 SNV sites from ICGC and COSMIC.
  Constructed novel module "Network".
  Included ~41,796,000 regulatory relationships (lncRNA).
  Included ~5,762,000 regulatory relationships (miRNA).
  Included ~12,739,000 regulatory relationships (ncRNA).
  Included ~90,889,000 regulatory relationships (mRNA).
  Constructed novel module "Enhancer".
  Included ~41,885,621 poised enhancer.
  Included ~8,975,669 active enhancer.
  Included ~141,511 super enhancer.
  Constructed novel module "EpiInter".
  Constructed novel module "Batch-Download".

Previous version 2.3.0 (2016-09-01)
Access to previous ChIPbase v2.0
  • ChIP-seq data: ~10,000
  • RNA-seq data: ~20,000

Sample Statistics in 5 Species

Human (Homo sapiens)          
Mouse (Mus musculus)    
Fruitfly (Drosophila melanogaster)  
Thale cress (Arabidopsis thaliana)    
Worm (Caenorhabditis elegans)