Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis
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Cistrome 数据浏览器：用于基因调控分析的扩展数据集和新工具
DOI：
10.1093/nar/gky1094
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发表时间：
2019-01-08
影响因子：
14.9
通讯作者：
Liu, X. Shirley
中科院分区：
文献类型：
--
作者：
Zheng, Rongbin;Wan, Changxin;Liu, X. Shirley
摘要：Cistrome数据浏览器（DB）是一个来源于ChIP-seq，DNase-seq和ATAC-seq染色质分析的人类和小鼠顺式调控信息的资源，这些分析绘制了转录因子结合位点，组蛋白翻译后修饰和染色质可进入核酸内切酶活性区域的全基因组位置。目前，Cistrome DB包含大约47，000个人类和小鼠样本，与两年前的上一个版本相比，新收集了大约24，000个数据集。此外，Cistrome DB有一个新的Toolkit模块，具有多个功能，允许用户更好地利用大规模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素。其次，顺反子DB工具包便于在任何给定的小于2 Mb的基因组间隔中搜索因子结合、组蛋白修饰和染色质可及性。第三，该工具包可以根据与用户提供的基因组间隔集的基因组间隔重叠来确定最相似的ChIP-seq、DNase-seq和ATAC-seq样本。该数据库是一个用户友好的，最新的，维护良好的资源，新的工具将大大有利于生物医学研究界。该数据库可在http：//cistrome.org/db上免费查阅，工具包可在http://dbtoolkit.cistrome.org上查阅。
Abstract 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.