School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
Institute of Oncologic Pathology, Medical College of Shantou University, Shantou 515041, China.
Nucleic Acids Res. 2019 Jul 2;47(W1):W248-W255. doi: 10.1093/nar/gkz302.
Super-enhancers (SEs) have prominent roles in biological and pathological processes through their unique transcriptional regulatory capability. To date, several SE databases have been developed by us and others. However, these existing databases do not provide downstream or upstream regulatory analyses of SEs. Pathways, transcription factors (TFs), SEs, and SE-associated genes form complex regulatory networks. Therefore, we designed a novel web server, SEanalysis, which provides comprehensive SE-associated regulatory network analyses. SEanalysis characterizes SE-associated genes, TFs binding to target SEs, and their upstream pathways. The current version of SEanalysis contains more than 330 000 SEs from more than 540 types of cells/tissues, 5042 TF ChIP-seq data generated from these cells/tissues, DNA-binding sequence motifs for ∼700 human TFs and 2880 pathways from 10 databases. SEanalysis supports searching by either SEs, samples, TFs, pathways or genes. The complex regulatory networks formed by these factors can be interactively visualized. In addition, we developed a customizable genome browser containing >6000 customizable tracks for visualization. The server is freely available at http://licpathway.net/SEanalysis.
超级增强子 (SEs) 通过其独特的转录调控能力在生物学和病理学过程中发挥着重要作用。迄今为止，我们和其他人已经开发了几个 SE 数据库。然而，这些现有的数据库并没有提供 SE 的下游或上游调控分析。通路、转录因子 (TFs)、SEs 和与 SE 相关的基因形成复杂的调控网络。因此，我们设计了一个新的网络服务器 SEanalysis，它提供了全面的 SE 相关调控网络分析。SEanalysis 描述了与 SE 相关的基因、与目标 SE 结合的 TF 及其上游通路。当前版本的 SEanalysis 包含来自 540 多种细胞/组织的超过 330000 个 SE、来自这些细胞/组织的 5042 个 TF ChIP-seq 数据、约 700 个人类 TF 的 DNA 结合序列基序和来自 10 个数据库的 2880 个通路。SEanalysis 支持通过 SE、样本、TFs、通路或基因进行搜索。这些因素形成的复杂调控网络可以进行交互式可视化。此外，我们开发了一个可定制的基因组浏览器，其中包含 >6000 个可定制的轨道用于可视化。该服务器可在 http://licpathway.net/SEanalysis 免费获得。
