Journal
EMBO REPORTS
Volume 19, Issue 12, Pages -Publisher
WILEY
DOI: 10.15252/embr.201846255
Keywords
ChIP-seq; data mining; DNase-seq; enhancer; transcription factor
Categories
Funding
- KAKENHI from the Japan Society for the Promotion of Science (JSPS) [25840087, 18KT0024, 16H06530, 26291051, 17H01571, 15K14529]
- AMED [JP17gm5010003]
- National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST)
- Grants-in-Aid for Scientific Research [17H01571, 25840087, 18KT0024, 26291051, 15K14529] Funding Source: KAKEN
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We have fully integrated public chromatin chromatin immunoprecipitation sequencing (ChIP-seq) and DNase-seq data (n > 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 (). 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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