Ch IP ‐Atlas: a data‐mining suite powered by full integration of public Ch IP ‐seq data
Top Cited Papers
Open Access
- 9 November 2018
- journal article
- research article
- Published by Springer Science and Business Media LLC in EMBO Reports
- Vol. 19 (12)
- https://doi.org/10.15252/embr.201846255
Abstract
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 (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.Keywords
Funding Information
- Japan Society for the Promotion of Science (25840087, 26291051, 17H01571, 15K14529, 18KT0024, 16H06530)
- Japan Agency for Medical Research and Development (JP17gm5010003)
- National Bioscience Database Center
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