Eukaryotic Promoter Database

The Eukaryotic Promoter Database (EPD) provides accurate transcription start site (TSS) information for promoters of 15 model organisms, from human to yeast to the malaria parasite Plasmodium falciparum. While the original database was a manually curated database based on published experiments, new promoter collections are now produced entirely automatically (under the name “EPDnew”) based on high-throughput transcript mapping data and high-quality gene annotation resources. Corresponding functional genomics data can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats like FASTA or BED for subsequent analysis with other tools; of note, EPD is tightly integrated with two tool suites developed by our group: ChIP-Seq and Signal Search Analysis, for analysis of chromatin context and sequence motif respectively. EPD provides promoter viewers, designed with the aim of integrating and displaying information from different sources about, for instance, histone marks, transcription factor-binding sites or SNPs with known phenotypes. These viewers rely upon the UCSC genome browser as a visualization platform, which enables users to view data tracks from EPD jointly with tracks from UCSC or public track hubs.真核启动子数据库（Eukaryotic Promoter Database, EPD）为15种模式生物的启动子提供精准的转录起始位点（transcription start site, TSS）信息，涵盖人类、酵母乃至恶性疟原虫（Plasmodium falciparum）等多个物种。初代数据库为基于已发表实验的人工审校数据库，而当前全新的启动子数据集（以“EPDnew”为名）则完全依托高通量转录本定位数据与高质量基因注释资源自动生成。配套的功能基因组学数据可通过基因组浏览器查看，亦可经由网页接口完成查询与分析，还能以FASTA、BED等标准格式导出，以供其他工具开展后续分析；值得关注的是，EPD与本团队开发的两款工具套件实现了深度整合：分别用于染色质环境分析的ChIP-Seq，以及用于序列基序分析的Signal Search Analysis。EPD还提供了启动子查看器，其设计初衷为整合并展示多源相关信息，例如组蛋白修饰标记、转录因子结合位点或携带已知表型的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）。此类查看器依托UCSC基因组浏览器作为可视化平台，支持用户将EPD的数据轨道与UCSC或公共轨道枢纽的轨道进行联合查看。

搜集汇总

背景与挑战

背景概述

Eukaryotic Promoter Database（EPD）是一个注释非冗余的真核POL II启动子数据库，其转录起始位点已通过实验确定。该数据库旨在为研究人员提供真核转录信号研究的支持，帮助分析基因调控机制。