Shanghai Key Laboratory of Tuberculosis, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.
Nucleic Acids Res. 2019 Jan 8;47(D1):D729-D735. doi: 10.1093/nar/gky1094.
The Cistrome Data Browser (DB) is a resource of human and mouse cis-regulatory information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays, which map the genome-wide locations of transcription factor binding sites, histone post-translational modifications and regions of chromatin accessible to endonuclease activity. Currently, the Cistrome DB contains approximately 47,000 human and mouse samples with about 24,000 newly collected datasets compared to the previous release two years ago. Furthermore, the Cistrome DB has a new Toolkit module with several features that allow users to better utilize the large-scale ChIP-seq, DNase-seq, and ATAC-seq data. First, users can query the factors which are likely to regulate a specific gene of interest. Second, the Cistrome DB Toolkit facilitates searches for factor binding, histone modifications, and chromatin accessibility in any given genomic interval shorter than 2Mb. Third, the Toolkit can determine the most similar ChIP-seq, DNase-seq, and ATAC-seq samples in terms of genomic interval overlaps with user-provided genomic interval sets. The Cistrome DB is a user-friendly, up-to-date, and well maintained resource, and the new tools will greatly benefit the biomedical research community. The database is freely available at http://cistrome.org/db, and the Toolkit is at http://dbtoolkit.cistrome.org.
染色质可及性数据库（Cistrome DB）是一个人类和小鼠顺式调控信息资源，来源于 ChIP-seq、DNase-seq 和 ATAC-seq 染色质谱分析，该资源可绘制转录因子结合位点、组蛋白翻译后修饰和内切酶活性可及染色质区域的全基因组位置图谱。目前，Cistrome DB 包含大约 47000 个人类和小鼠样本，与两年前的上一个版本相比，大约有 24000 个新收集的数据集。此外，Cistrome DB 还有一个新的 Toolkit 模块，具有几个功能，可以帮助用户更好地利用大规模的 ChIP-seq、DNase-seq 和 ATAC-seq 数据。首先，用户可以查询可能调节特定感兴趣基因的因子。其次，Cistrome DB Toolkit 可以在短于 2Mb 的任何给定基因组区间内进行因子结合、组蛋白修饰和染色质可及性的搜索。第三，Toolkit 可以根据与用户提供的基因组区间集的基因组区间重叠，确定最相似的 ChIP-seq、DNase-seq 和 ATAC-seq 样本。Cistrome DB 是一个用户友好、最新和维护良好的资源，新工具将极大地造福于生物医学研究社区。该数据库可免费在 http://cistrome.org/db 获得，Toolkit 可在 http://dbtoolkit.cistrome.org 获得。
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