The REDfly Database of Transcriptional Regulatory Elements

REDfly 转录调控元件数据库

• 批准号: 0843229
• 负责人: Marc Halfon
• 金额: $ 52.4万
• 依托单位: SUNY at Buffalo
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2012-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0843229&HistoricalAwards=false
• 关键词: REDfly; Database; Transcriptional; Regulatory; Elements

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).The State University of New York at Buffalo has received a grant to create a database and software tools to facilitate the study of gene regulation, through transcriptional cis-regulatory modules (CRMs). CRMs are a major class of genomic sequence elements required for the temporal and spatial control of gene expression. CRMs play critical roles with respect to normal phenotypic variation, birth defects, chronic diseases, and evolution. Despite this clear importance of CRMs for many areas of biology, our knowledge of these sequences is surprisingly limited. CRMs are vastly underrepresented in current genome annotations, in part because most CRMs are uncharacterized, but also because there has been little effort to curate the literature for known CRMs or to develop appropriate databases to house CRM information. This project, by producing a well-annotated collection of known CRMs, will be of significant use in a number of important areas, including studies of transcriptional regulation, of the evolution of CRMs and new gene functions, and of genome structure. The project also provides training data for computational approaches to CRM discovery, leading to improved methods for identifying uncharacterized CRMs. The project has constructed the first database of known CRMs for any animal, the REDfly (Regulatory Element Database for Fly) database of regulatory elements for the fruit fly Drosophila melanogaster. Funding under this award is allowing for the continued development and expansion of REDfly into a fully comprehensive resource for Drosophila and for its extension to regulatory elements from vertebrate model organisms, including the zebrafish and mouse. Analysis of the REDfly data will lead to the discovery of new important features of CRMs and to the generation of exciting new hypotheses about gene regulation that are being tested experimentally in the laboratory. REDfly also serves as a useful resource for education and training in genomics, gene regulation, and genome annotation at the graduate, undergraduate, and secondary school levels through a variety of courses, workshops, and informal training activities. These activities create in REDfly a comprehensive repository for cis-regulatory sequence and expression pattern data for three major metazoan model organisms, making REDfly the most powerful available resource for large-scale studies of the composition, organization, and evolution of transcriptional cis-regulatory elements.The REDfly database can be found at http://redfly.ccr.buffalo.edu.

该奖项是根据2009年美国复苏和再投资法案（公法111-5）资助的。纽约州立大学布法罗分校（State University of New York at Buffalo）获得了一笔拨款，用于创建一个数据库和软件工具，通过转录顺式调控模块（CRMs）促进基因调控的研究。crm是基因表达的时间和空间控制所需的基因组序列元件的主要类别。CRMs在正常表型变异、出生缺陷、慢性疾病和进化方面发挥着关键作用。尽管crm对生物学的许多领域具有明显的重要性，但我们对这些序列的了解却令人惊讶地有限。在当前的基因组注释中，CRM的代表性远远不足，部分原因是大多数CRM未被表征，但也因为很少有人努力整理已知CRM的文献或开发适当的数据库来存储CRM信息。这个项目，通过生产一个有良好注释的已知crm的集合，将在许多重要领域有重要的用途，包括转录调控的研究，crm的进化和新的基因功能，以及基因组结构。该项目还为发现客户关系管理的计算方法提供训练数据，从而改进识别未表征的客户关系管理的方法。该项目建立了第一个已知的动物调控因子数据库——果蝇调控元件数据库（REDfly）。该奖项的资金支持REDfly的持续发展和扩展，使其成为果蝇的全面资源，并将其扩展到脊椎动物模式生物（包括斑马鱼和老鼠）的调节元件。对红蝇数据的分析将导致发现crm的新的重要特征，并产生令人兴奋的关于基因调控的新假设，这些假设正在实验室进行实验测试。REDfly还通过各种课程、研讨会和非正式培训活动，为研究生、本科生和中学的基因组学、基因调控和基因组注释方面的教育和培训提供有用的资源。这些活动在REDfly中创建了三种主要后生动物模式生物的顺式调控序列和表达模式数据的综合存储库，使REDfly成为大规模研究转录顺式调控元件的组成、组织和进化的最强大的可用资源。REDfly数据库可以在http://redfly.ccr.buffalo.edu上找到。