rVarBase: an updated database for regulatory features of human variants.
rVarBase: an updated database for regulatory features of human variants.
复制标题
rVarBase：人类变异监管特征的更新数据库。
DOI：
10.1093/nar/gkv1107
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Wang J
中科院分区：
文献类型：
--
作者：
Guo L;Du Y;Qu S;Wang J
我们在这里提供了rVarBase数据库(http://rv.psych.ac.cn)，)，它是rSNPBase数据库的更新版本，可以为已知和新的人类变种提供可靠和详细的调控注释。这次更新扩大了数据库，包括其他类型的人类变异，如拷贝数变异(CNV)和新的变异，并包括其他类型的调控特征。现在rVarBase在三个维度上注释了变体：周围区域的染色质状态、重叠的调控元件和变体的潜在目标基因。引入了两种新的调节元件(lncRNAs和miRNA靶点)来提供额外的注释。提供了有关变异体在实验支持的TF结合区域(∼150bp)内重叠的转录因子结合位点(TFBs)(通常小于15bp)的详细信息，以及匹配的TF家族的结合基序。还增加了其他类型的扩展变体和与变体相关的表型。除了丰富数据内容外，还增加了以元素为中心的搜索模块，并改进了网络界面。总之，rVarBase拥有更多类型的人类变体，并包括更多类型的最新调控信息，以促进深入的功能研究，并为实验设计提供实用线索。
We present here the rVarBase database (http://rv.psych.ac.cn), an updated version of the rSNPBase database, to provide reliable and detailed regulatory annotations for known and novel human variants. This update expands the database to include additional types of human variants, such as copy number variations (CNVs) and novel variants, and include additional types of regulatory features. Now rVarBase annotates variants in three dimensions: chromatin states of the surrounding regions, overlapped regulatory elements and variants’ potential target genes. Two new types of regulatory elements (lncRNAs and miRNA target sites) have been introduced to provide additional annotation. Detailed information about variants’ overlapping transcription factor binding sites (TFBSs) (often less than 15 bp) within experimentally supported TF-binding regions (∼150 bp) is provided, along with the binding motifs of matched TF families. Additional types of extended variants and variant-associated phenotypes were also added. In addition to the enrichment in data content, an element-centric search module was added, and the web interface was refined. In summary, rVarBase hosts more types of human variants and includes more types of up-to-date regulatory information to facilitate in-depth functional research and to provide practical clues for experimental design.