ABI Sustaining: The REDfly database of transcriptional regulatory elements

转录顺式调节模块（CRMs）是调节基因表达所需的DNA序列-决定基因何时和何处被“打开”和“关闭”。标准物质在个体之间的正常变异、出生缺陷、慢性病和进化方面发挥着关键作用。尽管这些序列对生物学的许多领域具有明显的重要性，但这些序列并没有得到很好的记录。REDfly（苍蝇调控元件数据库）数据库通过为重要的研究生物果蝇（果蝇）管理已知的CRM和转录因子结合位点（TFBS），帮助填补了CRM注释中的这一空白。REDfly是现有最详细的动物调控元件注释平台。它的记录包括超过16，000个实验验证的CRM和2000个TFBS沿着以及它们的DNA序列，它们的相关基因和它们指导的基因表达模式。REDfly是基因组学，生物信息学和果蝇社区的一个使用良好且有价值的资源，是支持假设驱动的实证和计算研究的重要平台。它在与非果蝇以及果蝇系统相关的多个领域的许多研究中做出了贡献，包括CRM生物学，CRM发现，监管网络模型的构建，基因组数据集的解释和CRM进化。目前的项目将侧重于继续管理和维护数据库，使其保持最新状态，并为其用户发挥最大效用。这将确保REDfly继续作为分析、假设生成、评估和验证以及分子和发育生物学、遗传学、基因组学、生物信息学和进化方面的实证研究的重要原始数据来源。目前的项目也有一个宝贵的本科教育组成部分。它将继续成为布法罗大学“基因组注释”课程的重点，学生们将参与注释进入REDfly的调控元件，从而为研究界做出真正的贡献，同时学习基因组注释和生物定位技术以及基因调控科学。在一项新的努力中，一个REDfly单元将被引入巴鲁克学院-纽约市立大学的发育生物学课程，这是美国最多样化的校园之一。在课堂上表现出色的学生将被邀请到布法罗参加暑期本科生研究体验（SURE）计划，并担任REDfly策展人。这个持续奖的具体目标是让REDfly跟上文献中发现和报道的快速增加的CRM和TFBS数量，并以最大限度地发挥其对研究界的效用的方式维护REDfly网站。重点是：（1）管理。随着新研究的发表，REDfly将不断更新。重点仍将放在体内试验上，但在遇到和适当的情况下，将包括体外研究。(2)教育PI将继续使用REDfly作为他的“基因组注释”课程的基础。在巴鲁克学院-纽约市立大学的本科课程中将引入一个RED fly单元，每年夏天将最多两个课程的校友带到布法罗，作为布法罗医学院本科生暑期研究经验（SURE）计划的一部分，从事RED fly策展工作。(3)的服务. REDfly将继续以高度的响应能力为其用户社区服务，包括快速响应查询、自定义搜索和按需下载、纠错以及支持本科课程。(4)一般维修。通过识别和纠正编程错误，定期更新从FlyBase和其他来源导入的基因组注释，积极维护与外部资源的链接，软件和/或硬件更新等，REDfly将保持在最佳运行状态。REDfly数据库可以在www.example.com上找到http://redfly.ccr.buffalo.edu.This奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Transcriptional cis - regulatory modules (CRMs) are DNA sequences required for regulating gene expression - determining when and where genes are turned "on" and "off". CRMs play critical roles with respect to normal variation between individuals, birth defects, chronic diseases, and evolution. Despite the clear importance for many areas of biology, these sequences are not well-documented. The REDfly (Regulatory Element Database for Fly) database helps fill this gap in CRM annotation by curating known CRMs and transcription factor binding sites (TFBS) for the important research organism Drosophila melanogaster (fruit fly). REDfly is the most detailed existing platform for regulatory element annotation for any animal. It's records include over 16,000 experimentally verified CRMs and 2000 TFBSs along with their DNA sequence, their associated genes, and the gene expression patterns they direct. REDfly is a well-used and valuable resource for the genomics, bioinformatics, and Drosophila communities and is an important platform for supporting hypothesis-driven empirical and computational research. It has contributed to numerous studies in multiple areas relating to non-Drosophila as well as Drosophila systems including CRM biology, CRM discovery, construction of regulatory network models, interpretation of genomic datasets, and CRM evolution. The current project will focus on continued curation and maintenance of the database so that it remains up to date and functions with maximum utility for its users. This will ensure that REDfly continues to be available as an important source of raw data for analysis, hypothesis generation, assessment and validation, and empirical research in molecular and developmental biology, genetics, genomics, bioinformatics, and evolution. The current project also has a valuable undergraduate education component. It will continue to be the focus of a University at Buffalo course "Genome Annotation", in which the students participate in annotating regulatory elements for entry into REDfly, thus making genuine contributions to the research community while learning the techniques of genome annotation and biocuration and the science of gene regulation. In a new effort, a REDfly unit will be introduced into a Developmental Biology course at Baruch College-CUNY, one of the nation's most diverse campuses. Students who excel in the class will be invited to Buffalo to participate in the Summer Undergraduate Research Experience (SURE) program and serve as REDfly curators.The specific objectives of this Sustaining Award are to keep REDfly up to date with the rapidly increasing numbers of CRMs and TFBSs being discovered and reported in the literature, and to maintain the REDfly site in a manner that will maximize its utility to the research community. The focus is on: (1) Curation. REDfly will be kept up - to - date as new studies are published. Emphasis will remain on in vivo assays, but in vitro studies will be included where encountered and appropriate. (2) Education. The PI will continue to use REDfly as the basis for his "Genome Annotation" course. A REDfly unit will be introduced in an undergraduate course at Baruch College-CUNY, and bring up to two course alumni to Buffalo each summer to work on REDfly curation as a part of the University at Buffalo Medical School's Summer Research Experiences for Undergraduates (SURE) program. (3) Service. REDfly will continue to serve its user community with a high degree of responsiveness, including rapid response to queries, custom searches and downloads on request, error correction, and support for undergraduate courses. (4) General maintenance. REDfly will be maintained in peak operating condition through identification and correction of programming bugs, regular updates to genome annotations imported from FlyBase and other sources, active maintenance of links to outside resources, software and/or hardware updates, etc. These activities will ensure that REDfly data continue to be available as an important resource for the scientific community. The REDfly database can be found at http://redfly.ccr.buffalo.edu.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.