EPD in 2020: enhanced data visualization and extension to ncRNA promoters
EPD in 2020: enhanced data visualization and extension to ncRNA promoters
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DOI：
10.1093/nar/gkz1014
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Bucher, Philipp
中科院分区：
文献类型：
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作者：
Meylan, Patrick;Dreos, Rene;Bucher, Philipp
真核启动子数据库（EPD）可在https://epd.epfl.ch上在线获得，提供15种模式生物启动子的准确转录起始位点（TSS）信息以及相应的功能基因组学数据，这些数据可以在基因组浏览器中查看，通过网络界面查询或分析，或以标准格式（FASTA，BED，CSV）导出，用于随后使用其他工具进行分析。最近的工作集中在改进EPD启动子查看器，它使用UCSC基因组浏览器作为可视化平台。CAGE，ChIP-seq和类似数据的数千个高分辨率轨道已经生成并组织到公共轨道中心。定制的，可重复的启动子视图，结合EPD提供的轨道与本地UCSC基因组浏览器轨道，可以从生物体摘要页面或从单个启动子条目访问。此外，由于最近ncRNA基因目录的改进和稳定，我们能够发布来自人类和小鼠的某些类别的ncRNA的启动子集合。此外，我们开发了自动计算协议，根据配对末端（RAMPAGE）TSS映射数据将孤儿TSS峰分配给下游基因，这使我们能够向人类启动子集合中添加近9000个新条目。自从我们在这本杂志上发表的上一篇文章以来，EPD被扩展到另外五种模式生物：恒河猴、大鼠、狗、鸡和恶性疟原虫。
The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats (FASTA, BED, CSV) for subsequent analysis with other tools. Recent work has focused on the improvement of the EPD promoter viewers, which use the UCSC Genome Browser as visualization platform. Thousands of high-resolution tracks for CAGE, ChIP-seq and similar data have been generated and organized into public track hubs. Customized, reproducible promoter views, combining EPD-supplied tracks with native UCSC Genome Browser tracks, can be accessed from the organism summary pages or from individual promoter entries. Moreover, thanks to recent improvements and stabilization of ncRNA gene catalogs, we were able to release promoter collections for certain classes of ncRNAs from human and mouse. Furthermore, we developed automatic computational protocols to assign orphan TSS peaks to downstream genes based on paired-end (RAMPAGE) TSS mapping data, which enabled us to add nearly 9000 new entries to the human promoter collection. Since our last article in this journal, EPD was extended to five more model organisms: rhesusmonkey, rat, dog, chicken and Plasmodium falciparum.