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Cistrome DB specifications


Unique identifier OMICS_01853
Name Cistrome DB
Alternative names Cistrome Data Browser, CistromeMap, CistromeDB
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus



  • person_outline Liu Shirley
  • person_outline Clifford Meyer

Publications for Cistrome Data Browser

Cistrome DB citations


Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome

Nat Commun
PMCID: 5309719
PMID: 28169291
DOI: 10.1038/ncomms14400

[…] ne CRC line) as the background set (−bg option). For the analysis of experimentally determined TF binding sites in colon, ChIP-seq peak bed files for factors profiled in colon were retrieved from the Cistrome Data Browser. Coordinates were converted from hg38 to hg19 using the UCSC Genome Browser liftOver command line tool ( Gained […]


Nuclear Receptor Signaling Atlas: Opening Access to the Biology of Nuclear Receptor Signaling Pathways

PLoS One
PMCID: 4556694
PMID: 26325041
DOI: 10.1371/journal.pone.0135615

[…] ining tool to view relative expression levels in the context of transcription factor binding. Cistromic data pertinent to the NR field have been compiled within a beta version of the Nuclear Receptor Cistrome Data Browser (, and we will incorporate information from this resource and links to popular genome browsers cistromic and epigenomic tracks will be added in future releases. […]


A Computational Model for Histone Mark Propagation Reproduces the Distribution of Heterochromatin in Different Human Cell Types

PLoS One
PMCID: 3777982
PMID: 24069233
DOI: 10.1371/journal.pone.0073818

[…] nload from the provided internet sites. The available control file was used as control library. The data for HeLa cells was originally generated by refs. – and the bed files were downloaded using the CistromeMap interface ( We used the control library from . All positions were aligned to human reference genome hg18. […]


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Cistrome DB institution(s)
Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA; Biological and Biomedical Science Program, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
Cistrome DB funding source(s)
Supported by the National Key Research and Development Program of China [2016YFC1303200, 2017YFC0908500]; National Natural Science Foundation of China [31801110, 81573023]; National Institutes of Health of US [U24 HG009446 and U01 CA180980].

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