Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
School of Life Sciences, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland.
Nucleic Acids Res. 2020 Jan 8;48(D1):D65-D69. doi: 10.1093/nar/gkz1014.
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: rhesus monkey, rat, dog, chicken and Plasmodium falciparum.
真核启动子数据库（EPD）可在 https://epd.epfl.ch 在线获取，为 15 种模式生物的启动子提供准确的转录起始位点（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，以便与其他工具进行后续分析。最近的工作重点是改进 EPD 启动子查看器，这些查看器使用 UCSC 基因组浏览器作为可视化平台。已经生成了数千个用于 CAGE、ChIP-seq 等数据的高分辨率跟踪，并将其组织到公共跟踪集线器中。可以从生物体摘要页面或单个启动子条目访问结合 EPD 提供的跟踪和本地 UCSC 基因组浏览器跟踪的定制、可重复的启动子视图。此外，由于最近对 ncRNA 基因目录的改进和稳定，我们能够从人类和小鼠中发布某些类 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，这使我们能够将近 9000 个新条目添加到人类启动子集合中。自我们上次在该期刊上发表文章以来，EPD 已扩展到另外 5 种模式生物：恒河猴、大鼠、狗、鸡和恶性疟原虫。
