ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
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Abstract
> 70,000) derived from six representative model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast), and have devised a data-mining platform-designated ChIP-Atlas (http://chip-atlas.org). ChIP-Atlas is able to show alignment and peak-call results for all public ChIP-seq and DNase-seq data archived in the NCBI Sequence Read Archive (SRA), which encompasses data derived from GEO, ArrayExpress, DDBJ, ENCODE, Roadmap Epigenomics, and the scientific literature. All peak-call data are integrated to visualize multiple histone modifications and binding sites of transcriptional regulators (TRs) at given genomic loci. The integrated data can be further analyzed to show TR-gene and TR-TR interactions, as well as to examine enrichment of protein binding for given multiple genomic coordinates or gene names. ChIP-Atlas is superior to other platforms in terms of data number and functionality for data mining across thousands of ChIP-seq experiments, and it provides insight into gene regulatory networks and epigenetic mechanisms.
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The record
- Venue
- EMBO Reports
- Topic
- Genomics and Phylogenetic Studies
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- —
- Funders
- National Bioscience Database CenterJapan Science and Technology AgencyJapan Society for the Promotion of ScienceMinistry of Education, Culture, Sports, Science and TechnologyInstitute of GeneticsJapan Agency for Medical Research and Development
- Keywords
- SuiteComputer scienceDatabaseGeography
- Has abstract in OpenAlex
- yes