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ChIP-Atlas specifications


Unique identifier OMICS_15124
Name ChIP-Atlas
Restrictions to use None
Community driven No
Data access Application programming interface
User data submission Not allowed
Maintained Yes


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus



  • person_outline Shinya Oki

ChIP-Atlas citations


Common α globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease

PLoS Genet
PMCID: 5891078
PMID: 29590102
DOI: 10.1371/journal.pgen.1007293

[…] redict the function of non-coding variants and were used as previously described to in silico predict the effect of common variants.[, , , ] In silico mutagenesis was performed as described in [].The ChIP-Atlas resource as well as K562 experiments from the ENCODE project were used to search for DHS and transcription factor (TF) occupancy in blood-based tissues.[, ] TF binding motif disruptions wer […]


Systems epigenomics inference of transcription factor activity implicates aryl hydrocarbon receptor inactivation as a key event in lung cancer development

Genome Biol
PMCID: 5738803
PMID: 29262847
DOI: 10.1186/s13059-017-1366-0

[…] y not be direct binding targets of the TF, but could equally well represent indirect downstream targets which faithfully measure upstream TF binding activity. To investigate this further, we used the ChIP-Atlas ( resource, which contains > 25,000 chromatin immunoprecipitation sequencing (ChIP-seq) profiles, including those from ENCODE and the NIH Roadmap (see “”). For a total […]


miR‐155 induces ROS generation through downregulation of antioxidation‐related genes in mesenchymal stem cells

Aging Cell
PMCID: 5676067
PMID: 28967703
DOI: 10.1111/acel.12680

[…], TargetScan (, and miRPath ( In silico ChIP‐seq analysis was performed using ChIP‐Atlas (DBCLS, Tokyo, Japan and Kyusyu University, Fukuoka, Japan) and Integrative Genomics Viewer Ver2.3.89 (Broad Institute, Cambridge, MA, USA) with GEO dataset GSE79813 (Meyer et al., ). […]


The PDGFRα laminin B1 keratin 19 cascade drives tumor progression at the invasive front of human hepatocellular carcinoma

PMCID: 5702717
PMID: 28783171
DOI: 10.1038/onc.2017.260

[…] Analysis was performed using the web-based tool cBioPortal., Publically available ChIP-seq data for TEAD4 in HepG2 cells (GEO accession GSM1010875) were downloaded from ChIP-Atlas ( BigWig and Peak-calls (q<1E-05) were visualized in the Integrative Genomics Viewer. […]


ChIP seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network

PMCID: 5482983
PMID: 28455373
DOI: 10.1242/dev.143479

[…] pt for band width, which was 150 bases. External data (Table S4) were analyzed using the default settings. The Bowtie-aligned peaks and MACS-determined peak positions were visualized using IGV () and ChIP-Atlas ( The above data processing was performed using the software package SraTailor (). Peak overlaps were analyzed using Galaxy (), and the genomic spans given in BED for […]


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