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
• 负责人: MARC S HALFON
• 金额: $ 47.17万
• 依托单位: STATE UNIVERSITY OF NEW YORK AT BUFFALO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-20 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10267371
• 关键词: Acute Disease; Anatomy; Area; Arthropods; Attention; Binding Sites; Biocontrols; Bioinformatics; Biology; Biotechnology; Chronic Disease; Collection; Communities; Complex; Computer software; Congenital Abnormality; DNA Sequence; Data; Data Analyses; Databases; Development; Developmental Biology; Drosophila genome; Drosophila genus; Ectopic Expression; Elements; Empirical Research; Enhancers; Environment; Evolution; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Generations; Genes; Genetic; Genetic Transcription; Genomics; Goals; Insect Control; Insecta; Knowledge; Link; Literature; Machine Learning; Metadata; Methods; Mission; Modeling; Molecular Biology; Ontology; Paper; Phenotype; Play; Public Health; Publications; Publishing; Records; Regulator Genes; Regulatory Element; Reporting; Research; Resources; Role; Site; Source; Staging; Structure; Training; Transcriptional Regulation; Update; Validation; Variant; base; biomedical ontology; data integration; data modeling; fly; genome annotation; genome browser; genome sequencing; genomic data; improved; insect disease vector; knowledge base; model organisms databases; ontology development; pathogen; promoter; sex; transcription factor; transmission process; user-friendly

We have developed a unique resource, the REDfly (Regulatory Element Database for Fly) database of transcriptional regulatory elements, to provide regulatory annotation for the genome of Drosophila and other insects. The genomic sequences regulating gene expression—transcriptional cis-regulatory modules (CRMs, e.g. “enhancers”) and transcription factor binding sites (TFBSs)—are not currently curated by any other 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 large-scale genomics projects, providing training data for machine-learning CRM- discovery methods, genome annotation, modeling gene regulatory networks, studying the evolution of gene regulation, and numerous aspects of the basic biology of transcriptional regulation. Knowledge of insect CRMs is also an important step in developing biotechnology methods for control of insect disease vectors and for eliminating pathogen transmission. REDfly includes experimentally verified CRMs and TFBSs along with their DNA sequence, their associated genes, and the expression patterns they direct. It is the most detailed existing platform for metazoan regulatory element annotation and is widely acknowledged as the premier resource in the regulatory genomics arena. Only REDfly integrates all of the available insect cis-regulatory information from multiple sources to provide a comprehensive collection of regulatory elements. The objectives of this proposal are to keep REDfly up to date with the rapidly increasing numbers of CRMs and TFBSs being identified 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, and valuable data and metadata will be added to existing records. (2) User interface. We will develop more sophisticated search, display, and download capabilities to keep pace with the vastly increased amounts and types of data now contained in the database. We will update software components that have become obsolete in the decade since their initial implementation. (3) Data integration. We will increase integration of disparate data types and develop confidence scores for annotations. (4) Workflow. We will increase our curation efficiency and ability through improved workflows. (5) Ontology support. We will improve how we use biomedical ontologies through incorporating the latest ontology- related software, including ontology browsers and SPARQL queries. The proposed activities are significant as they will keep up-to-date a high-value resource for multiple research communities and increase REDfly’s utility by adding needed new features and functions. 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. It will have greatly increased impact through the updates and enhancements proposed here.

我们开发了一个独特的资源，REDfly（苍蝇监管元素数据库）数据库， 转录调控元件，为果蝇和其他基因组提供调控注释， 昆虫调节基因表达的基因组序列-转录顺式调节模块（CRMs， 例如“增强子”）和转录因子结合位点（TFBS）-目前没有任何其他主要的 数据库资源。这是一个严重的缺陷，因为CRM在出生缺陷方面发挥着关键作用， 慢性疾病以及正常发育、表型变异和进化。知识 实验验证的标准物质和TFBS是至关重要的许多研究领域，包括解释和 验证大规模基因组学项目开发的数据，为机器学习CRM提供训练数据- 发现方法，基因组注释，基因调控网络建模，基因进化研究 调节，以及转录调节的基础生物学的许多方面。昆虫标准物质知识 这也是发展生物技术方法控制昆虫病媒和 消除病原体传播。REDfly包括经过实验验证的CRM和TFBS沿着， DNA序列、相关基因及其指导的表达模式。它是现存最详细的 后生动物调控元件注释的平台，并被广泛认为是 调控基因组学竞技场。只有REDfly整合了所有可用的昆虫顺式调控信息， 多个来源，以提供监管要素的全面集合。本提案的目标 是为了使REDfly保持最新状态，以识别快速增加的CRM和TFBS数量，并 更新REDfly网站，以最大限度地发挥其对研究界的效用。重点是：（1）管理。REDfly 随着新研究的发表，将继续更新，并将增加有价值的数据和元数据 现有记录。(2)用户界面.我们将开发更复杂的搜索、显示和下载 数据库中包含的数据量和数据类型大幅增加， 我们将更新自最初实施以来的十年中已经过时的软件组件。 (3)数据整合。我们将增加不同数据类型的集成，并为 注释。(4)工作流我们将通过改进工作流程来提高我们的策展效率和能力。（五） 本体支持。我们将通过整合最新的本体来改进我们如何使用生物医学本体- 相关软件，包括本体浏览器和SPARQL查询。拟议的活动意义重大， 他们将为多个研究团体保持最新的高价值资源，并增加REDfly的效用 添加所需的新特性和功能。REDfly已经证明了其重要和独特的价值 作为一个重要的平台，支持假设驱动的实证和计算研究，在多个 研究领域。通过这里提出的更新和增强，它将大大增加影响力。