Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
Database Center for Life Science, Joint-Support Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan.
EMBO Rep. 2018 Dec;19(12). doi: 10.15252/embr.201846255. Epub 2018 Nov 9.
We have fully integrated public chromatin chromatin immunoprecipitation sequencing (ChIP-seq) and DNase-seq data ( > 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.
我们已经完全整合了来自六个代表性模式生物（人类、小鼠、大鼠、果蝇、线虫和 budding yeast）的公共染色质免疫沉淀测序（ChIP-seq）和 DNase-seq 数据（>70,000），并设计了一个数据挖掘平台，命名为 ChIP-Atlas（http://chip-atlas.org）。ChIP-Atlas 能够显示在 NCBI Sequence Read Archive（SRA）中归档的所有公共 ChIP-seq 和 DNase-seq 数据的对齐和峰调用结果，这些数据涵盖了来自 GEO、ArrayExpress、DDBJ、ENCODE、Roadmap Epigenomics 和科学文献的数据。所有峰调用数据都被整合在一起，以可视化给定基因组位置的多个组蛋白修饰和转录调节因子（TR）的结合位点。整合的数据可以进一步分析，以显示 TR-基因和 TR-TR 相互作用，以及检查给定多个基因组坐标或基因名称的蛋白质结合的富集情况。在数据挖掘数千个 ChIP-seq 实验方面，ChIP-Atlas 在数据数量和功能方面优于其他平台，它为基因调控网络和表观遗传机制提供了深入的了解。
