ABI Sustaining: The REDfly database of transcriptional regulatory elements

ABI Sustaining：转录调控元件的 REDfly 数据库

• 批准号: 1355511
• 负责人: Marc Halfon
• 金额: $ 44.74万
• 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: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2018-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1355511&HistoricalAwards=false
• 关键词: ABI; Sustaining; REDfly; database; transcriptional

The State University of New York at Buffalo is awarded a sustaining grant to support ongoing operation of The REDfly (Regulatory Element Database for Fly). REDfly is a freely available and easily web-accessible resource of significant value to the biological community, both for wet-lab biologists and for bio-informaticians. Undergraduate students will play a significant role in this project as the primary curators for ongoing regulatory element annotation. In addition, REDfly has a demonstrated utility for education and training. REDfly has been the source of data for student projects in bioinformatics/computational biology at several schools. It is also the focus of a seminar course for undergraduates taught by the PI, "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. The students learn how to use an array of web-based sequence analysis tools, gain an appreciation for the complexities of gene expression and anatomy, develop skills in reading the primary literature, and are exposed to a diversity of experimental systems and approaches.Transcriptional cis-regulatory modules (CRMs) are a major class of genomic sequence elements 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 of CRMs for many areas of biology, these sequences are vastly underrepresented in current genome annotations. REDfly 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. Its records include over 1850 experimentally verified CRMs and 2000 TFBSs along with their DNA sequence, their associated genes, and the 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 of the database and is anticipated to increase the number of records by five-fold or more. 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 REDfly Database can be found at http://redfly.ccr.buffalo.edu.

位于布法罗的纽约的州立大学获得了一笔持续资助，以支持REDfly（苍蝇监管元素数据库）的持续运作。REDfly是一个免费提供的，易于访问的网络资源，对生物界具有重要价值，无论是湿实验室生物学家还是生物信息学家。本科生将在这个项目中发挥重要作用，作为正在进行的监管元素注释的主要策展人。此外，REDfly在教育和培训方面也有明显的效用。REDfly一直是几所学校生物信息学/计算生物学学生项目的数据来源。它也是PI教授的本科生研讨会课程的重点，“基因组注释”，学生参与注释进入REDfly的调控元件，从而为研究社区做出真正的贡献，同时学习基因组注释和生物定位技术以及基因调控科学。学生学习如何使用一系列基于网络的序列分析工具，了解基因表达和解剖学的复杂性，培养阅读主要文献的技能，转录顺式调控模块（CRMs）是调控基因表达所需的主要一类基因组序列元件，决定基因何时何地转向。开和关。“CRM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CRM对于生物学的许多领域具有明显的重要性，但这些序列在当前的基因组注释中被大大低估。REDfly通过为重要的研究生物果蝇（果蝇）策划已知的CRM和转录因子结合位点（TFBS）来填补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1850个实验验证的CRM和2000个TFBS沿着，以及它们的DNA序列、相关基因和它们指导的表达模式。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数据库，预计记录数量将增加五倍或更多。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。REDfly数据库可在http://redfly.ccr.buffalo.edu上找到。