REDfly: The regulatory sequence resource for Drosophila and other insects

 描述(由申请人提供)： 调控基因表达的基因组序列--转录顺式调节模块(CRM)和转录因子结合位点(TFBs)--在当前的基因组注释中表现得很差，而且这些功能目前还没有被任何主要的数据库资源管理。这是一个严重的缺陷，因为CRM在出生缺陷和慢性病以及正常发育、表型变异和进化方面发挥着关键作用。对经过实验验证的CRM和TFBs的了解对许多研究领域至关重要，包括解释和验证由ENCODE和modENCODE项目、GWAS研究和其他大型基因组学项目开发的数据。我们开发了一个独特的资源，REDFly(Fly的调控元素数据库)数据库，以帮助填补CRM注释中的这一空白。REDFly包括经过实验验证的CRM和TFBS以及它们的DNA序列、它们的相关基因和它们指导的表达模式。只有REDFly整合了来自多个来源的所有可用果蝇顺式调控信息，以提供全面的调控元件集合。REDFly是现有的后生动物调控元件注释最详细的平台，被广泛认为是调控基因组学领域的首要资源。这项建议的目的是使REDly跟上正在确定的快速增加的CRM和TFBs的数量，扩大REDly对重要的监管特征类型和它为其收集数据的物种的覆盖范围，并更新REDly的网站，以最大限度地提高其对研究界的效用。研究的重点是：(1)培养。随着新研究的发表，REDly将继续保持最新状态。(2)用户界面。将实施更灵活的搜索、显示和下载功能，以确保所有数据都可以轻松搜索、显示和下载。(3)扩展到其他昆虫。来自其他昆虫物种的数据，包括重要的疾病媒介，如冈比亚按蚊和埃及伊蚊，目前数据有限，但增长迅速。REDFly将创建结构来保存来自其他昆虫物种的调控序列的数据，这也将允许未来容易地扩展到任何生物体。(4)工具。REDFly将开发处理REDFly特有数据的内置工具和一系列工作流程，以促进使用Galaxy平台将REDFly数据与其他基因组数据相结合，例如来自modENCODE和各种模式生物体数据库的数据。拟议的活动意义重大，因为它们将为多个研究界带来最新的宝贵资源，通过增加必要的新功能和工具来增加其效用，并通过增加对更多生物的支持来扩大其相关性。REDFly已经证明了它作为一个重要的平台在多个研究领域支持假设驱动的经验和计算研究的基本和独特的价值，并将通过这里提出的更新和增强大大增加影响。

 DESCRIPTION (provided by applicant): The genomic sequences regulating gene expression-transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs)-are poorly represented in current genome annotations, and these features are not currently curated by any major database resources. This is a serious deficiency as CRMs play critical roles with respect to birth defects and chronic diseases as well as normal development, phenotypic variation, and evolution. Knowledge of experimentally validated CRMs and TFBSs is vital for many areas of research including interpretation and validation of data developed by the ENCODE and modENCODE projects, by GWAS studies, and by other large-scale genomics projects. We have developed a unique resource, the REDfly (Regulatory Element Database for Fly) database of Drosophila transcriptional regulatory elements, to help fill this gap in CRM annotation. REDfly includes experimentally verified CRMs and TFBSs along with their DNA sequence, their associated genes, and the expression patterns they direct. Only REDfly integrates all of the available cis-regulatory information for Drosophila from multiple sources to provide a comprehensive collection of regulatory elements. REDfly is the most detailed existing platform for metazoan regulatory element annotation and is widely acknowledged as the premier resource in the regulatory genomics arena. The objective of this proposal is to keep REDfly up to date with the rapidly increasing numbers of CRMs and TFBSs being identified, to increase REDfly's coverage of important regulatory feature types and of the species for which it collects data, and to update the REDfly site to maximize its utility to the research community. The focus is on: (1) Curation. REDfly will continue to be kept up-to-date as new studies are published. (2) User interface. More flexible search, display, and download capabilities will be implemented to ensure that all data can be easily searched, displayed, and downloaded. (3) Expansion to other insects. Data from other insect species, including important disease vectors such as the mosquitoes Anopheles gambiae and Aedes aegypti, are currently limited but rapidly growing. REDfly will create structures to hold data for regulatory sequences from other insect species, which will also allow for easy future expansion to any organism. (4) Tools. REDfly will develop built-in tools for manipulating REDfly-specific data and a series of workflows to facilitate use of the Galaxy platform for integrating REDfly data with other genomic data, e.g. from modENCODE and various model organism databases. The proposed activities are significant as they will bring up-to-date a valuable resource for multiple research communities, increase its utility by adding needed new features and tools, and expand its relevance by adding support for additional organisms. REDfly has already demonstrated its essential and unique value as an important platform for supporting hypothesis-driven empirical and computational research in multiple research areas and will have greatly increased impact through the updates and enhancements proposed here.