TY - JOUR
T1 - ChIP-Atlas
T2 - a data-mining suite powered by full integration of public ChIP-seq data
AU - Oki, Shinya
AU - Ohta, Tazro
AU - Shioi, Go
AU - Hatanaka, Hideki
AU - Ogasawara, Osamu
AU - Okuda, Yoshihiro
AU - Kawaji, Hideya
AU - Nakaki, Ryo
AU - Sese, Jun
AU - Meno, Chikara
N1 - Funding Information:
The public data used in this research were obtained from SRA of NCBI. Computations were performed mostly on the NIG supercomputer at ROIS National Institute of Genetics. This work was supported by KAKENHI grants 25840087, 18KT0024, 16H06530, 26291051, 17H01571, and 15K14529 from the Japan Society for the Promotion of Science (JSPS); by AMED under grant number JP17gm5010003; and by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).
Publisher Copyright:
© 2018 The Authors. Published under the terms of the CC BY 4.0 license
PY - 2018/12
Y1 - 2018/12
N2 - 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.
AB - 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.
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U2 - 10.15252/embr.201846255
DO - 10.15252/embr.201846255
M3 - Article
C2 - 30413482
AN - SCOPUS:85056303744
SN - 1469-221X
VL - 19
JO - EMBO Reports
JF - EMBO Reports
IS - 12
M1 - e46255
ER -