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

Shinya Oki, Tazro Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, Chikara Meno

研究成果: ジャーナルへの寄稿記事

25 引用 (Scopus)

抄録

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.

元の言語英語
記事番号e46255
ジャーナルEMBO Reports
19
発行部数12
DOI
出版物ステータス出版済み - 12 2018

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Data Mining
Atlases
Chromatin Immunoprecipitation
Chromatin
Data mining
Deoxyribonucleases
Epigenomics
Histone Code
Literature
Saccharomycetales
Genes
Gene Regulatory Networks
Nucleic Acid Databases
Protein Binding
Diptera
Names
Fruit
Fruits
Binding Sites
Histones

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Genetics

これを引用

ChIP-Atlas : a data-mining suite powered by full integration of public ChIP-seq data. / Oki, Shinya; Ohta, Tazro; Shioi, Go; Hatanaka, Hideki; Ogasawara, Osamu; Okuda, Yoshihiro; Kawaji, Hideya; Nakaki, Ryo; Sese, Jun; Meno, Chikara.

:: EMBO Reports, 巻 19, 番号 12, e46255, 12.2018.

研究成果: ジャーナルへの寄稿記事

Oki, S, Ohta, T, Shioi, G, Hatanaka, H, Ogasawara, O, Okuda, Y, Kawaji, H, Nakaki, R, Sese, J & Meno, C 2018, 'ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data', EMBO Reports, 巻. 19, 番号 12, e46255. https://doi.org/10.15252/embr.201846255
Oki, Shinya ; Ohta, Tazro ; Shioi, Go ; Hatanaka, Hideki ; Ogasawara, Osamu ; Okuda, Yoshihiro ; Kawaji, Hideya ; Nakaki, Ryo ; Sese, Jun ; Meno, Chikara. / ChIP-Atlas : a data-mining suite powered by full integration of public ChIP-seq data. :: EMBO Reports. 2018 ; 巻 19, 番号 12.
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