Khan Aziz, Zhang Xuegong
MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.
MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China School of Life Sciences, Tsinghua University, Beijing 100084, China
Nucleic Acids Res. 2016 Jan 4;44(D1):D164-71. doi: 10.1093/nar/gkv1002. Epub 2015 Oct 4.
Super-enhancers are clusters of transcriptional enhancers that drive cell-type-specific gene expression and are crucial to cell identity. Many disease-associated sequence variations are enriched in super-enhancer regions of disease-relevant cell types. Thus, super-enhancers can be used as potential biomarkers for disease diagnosis and therapeutics. Current studies have identified super-enhancers in more than 100 cell types and demonstrated their functional importance. However, a centralized resource to integrate all these findings is not currently available. We developed dbSUPER (http://bioinfo.au.tsinghua.edu.cn/dbsuper/), the first integrated and interactive database of super-enhancers, with the primary goal of providing a resource for assistance in further studies related to transcriptional control of cell identity and disease. dbSUPER provides a responsive and user-friendly web interface to facilitate efficient and comprehensive search and browsing. The data can be easily sent to Galaxy instances, GREAT and Cistrome web-servers for downstream analysis, and can also be visualized in the UCSC genome browser where custom tracks can be added automatically. The data can be downloaded and exported in variety of formats. Furthermore, dbSUPER lists genes associated with super-enhancers and also links to external databases such as GeneCards, UniProt and Entrez. dbSUPER also provides an overlap analysis tool to annotate user-defined regions. We believe dbSUPER is a valuable resource for the biology and genetic research communities.
超级增强子是驱动细胞类型特异性基因表达的转录增强子簇，对细胞特性至关重要。许多与疾病相关的序列变异在疾病相关细胞类型的超级增强子区域中富集。因此，超级增强子可作为疾病诊断和治疗的潜在生物标志物。目前的研究已经在100多种细胞类型中鉴定出超级增强子，并证明了它们的功能重要性。然而，目前还没有一个集中的资源来整合所有这些发现。我们开发了dbSUPER（http://bioinfo.au.tsinghua.edu.cn/dbsuper/），这是第一个超级增强子的综合交互式数据库，其主要目标是提供一种资源，以协助开展与细胞特性和疾病转录调控相关的进一步研究。dbSUPER提供了一个响应式且用户友好的网页界面，以方便进行高效且全面的搜索和浏览。数据可以轻松发送到Galaxy实例、GREAT和Cistrome网络服务器进行下游分析，也可以在UCSC基因组浏览器中可视化，在那里可以自动添加自定义轨迹。数据可以以多种格式下载和导出。此外，dbSUPER列出了与超级增强子相关的基因，并链接到外部数据库，如GeneCards、UniProt和Entrez。dbSUPER还提供了一个重叠分析工具来注释用户定义的区域。我们相信dbSUPER是生物学和遗传学研究界的宝贵资源。
