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ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data.


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.

SUBMITTER: Oki S 

PROVIDER: S-EPMC6280645 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data.

Oki Shinya S   Ohta Tazro T   Shioi Go G   Hatanaka Hideki H   Ogasawara Osamu O   Okuda Yoshihiro Y   Kawaji Hideya H   Nakaki Ryo R   Sese Jun J   Meno Chikara C  

EMBO reports 20181109 12


We have fully integrated public chromatin chromatin immunoprecipitation sequencing (ChIP-seq) and DNase-seq data (<i>n</i> > 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 d  ...[more]

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