The REDfly Database of Transcriptional Regulatory Elements

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。布法罗的纽约州立大学获得了一笔赠款，用于创建一个数据库和软件工具，通过转录顺式调控模块（CRM）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。标准物质在正常表型变异、出生缺陷、慢性疾病和进化方面发挥着关键作用。尽管CRM对于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。CRM在目前的基因组注释中的代表性大大不足，部分原因是大多数CRM都没有特征，但也因为很少努力为已知的CRM整理文献或开发适当的数据库来容纳CRM信息。这个项目，通过生产一个良好的注释收集已知的标准物质，将在一些重要的领域，包括转录调控的研究，标准物质和新的基因功能的进化，以及基因组结构的显着使用。该项目还为CRM发现的计算方法提供了训练数据，从而改进了识别未表征CRM的方法。该项目构建了第一个已知的动物CRM数据库，即果蝇（Drosophila melanogaster）调控元件的REDfly（苍蝇调控元件数据库）数据库。该奖项下的资金允许继续开发和扩展REDfly，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（包括斑马鱼和小鼠）的调控元件。对REDfly数据的分析将导致发现CRM的新的重要特征，并产生关于基因调控的令人兴奋的新假设，这些假设正在实验室中进行实验测试。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教育和培训提供有用的资源。这些活动在REDfly中为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创建了一个全面的存储库，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。http://redfly.ccr.buffalo.edu

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.