REDfly: The regulatory sequence resource for Drosophila and other insects

REDfly:果蝇和其他昆虫的调控序列资源

基本信息

  • 批准号:
    9215682
  • 负责人:
  • 金额:
    $ 30.53万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2016
  • 资助国家:
    美国
  • 起止时间:
    2016-02-05 至 2019-12-31
  • 项目状态:
    已结题

项目摘要

 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.
 描述(由申请人提供): 调节基因表达的基因组序列-转录顺式调控模块(CRM)和转录因子结合位点(TFBS)-在当前的基因组注释中表现不佳,并且这些功能目前没有任何主要的数据库资源。这是一个严重的缺陷,因为标准物质在出生缺陷和慢性疾病以及正常发育、表型变异和进化方面发挥着关键作用。实验验证的CRM和TFBS的知识是至关重要的许多领域的研究,包括解释和验证的数据开发的ENCODE和modENCODE项目,GWAS研究,和其他大规模的基因组学项目。我们开发了一个独特的资源,果蝇转录调控元件的REDfly(果蝇调控元件数据库)数据库,以帮助填补CRM注释的这一空白。REDfly包括实验验证的CRM和TFBS沿着及其DNA序列、相关基因和它们指导的表达模式。只有REDfly整合了果蝇从多个来源获得的所有可用的顺式调控信息,以提供全面的调控元件集合。REDfly是后生动物调控元件注释的最详细的现有平台,被广泛认为是调控基因组学竞技场的首要资源。该提案的目的是使REDfly保持最新,以识别快速增加的CRM和TFBS数量,增加REDfly对重要监管特征类型和收集数据的物种的覆盖范围,并更新REDfly网站,以最大限度地提高其对研究界的效用。重点是:(1)管理。随着新研究的发表,REDfly将继续保持最新状态。(2)用户界面.将实现更灵活的搜索、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。关于其他昆虫物种,包括冈比亚按蚊和埃及伊蚊等重要病媒的数据目前有限,但正在迅速增长。REDfly将创建结构来保存其他昆虫物种的调控序列数据,这也将允许未来轻松扩展到任何生物。(4)工具. REDfly将开发用于操作REDfly特定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整合,例如来自modENCODE和各种模式生物数据库。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,通过增加所需的新功能和工具来增加其效用,并通过增加对其他生物的支持来扩大其相关性。REDfly已经证明了其作为支持多个研究领域中假设驱动的实证和计算研究的重要平台的重要和独特价值,并将通过此处提出的更新和增强功能大大增加影响力。

项目成果

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MARC S HALFON其他文献

MARC S HALFON的其他文献

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{{ truncateString('MARC S HALFON', 18)}}的其他基金

REDfly: The regulatory sequence resource for Drosophila and other insects
REDfly:果蝇和其他昆虫的调控序列资源
  • 批准号:
    10267371
  • 财政年份:
    2021
  • 资助金额:
    $ 30.53万
  • 项目类别:
REDfly: The regulatory sequence resource for Drosophila and other insects
REDfly:果蝇和其他昆虫的调控序列资源
  • 批准号:
    9024852
  • 财政年份:
    2016
  • 资助金额:
    $ 30.53万
  • 项目类别:
Regulatory element discovery in Anopheles gambiae
冈比亚按蚊调控元件的发现
  • 批准号:
    9165377
  • 财政年份:
    2016
  • 资助金额:
    $ 30.53万
  • 项目类别:
High sensitivity discovery of cis-regulatory modules
高灵敏度发现顺式调控模块
  • 批准号:
    7905876
  • 财政年份:
    2008
  • 资助金额:
    $ 30.53万
  • 项目类别:
High sensitivity discovery of cis-regulatory modules
高灵敏度发现顺式调控模块
  • 批准号:
    8303253
  • 财政年份:
    2008
  • 资助金额:
    $ 30.53万
  • 项目类别:
High sensitivity discovery of cis-regulatory modules
高灵敏度发现顺式调控模块
  • 批准号:
    7661575
  • 财政年份:
    2008
  • 资助金额:
    $ 30.53万
  • 项目类别:
High sensitivity discovery of cis-regulatory modules
高灵敏度发现顺式调控模块
  • 批准号:
    8119766
  • 财政年份:
    2008
  • 资助金额:
    $ 30.53万
  • 项目类别:
High sensitivity discovery of cis-regulatory modules
高灵敏度发现顺式调控模块
  • 批准号:
    7506876
  • 财政年份:
    2008
  • 资助金额:
    $ 30.53万
  • 项目类别:
Empirical assessment of analysis methods for DNA microarrays
DNA 微阵列分析方法的实证评估
  • 批准号:
    7197064
  • 财政年份:
    2007
  • 资助金额:
    $ 30.53万
  • 项目类别:
Computational and Functional Analysis of Gene Networks
基因网络的计算和功能分析
  • 批准号:
    7076196
  • 财政年份:
    2002
  • 资助金额:
    $ 30.53万
  • 项目类别:

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