Gene Regulation E. coli Database Integrated Modeling

基因调控大肠杆菌数据库集成建模

• 批准号: 7683918
• 负责人: Julio Collado-Vides
• 金额: $ 40.05万
• 依托单位: CENTER FOR GENOMIC SCIENCES
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-08-01 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7683918
• 关键词: Affect; Area; Bacteria; Bacterial Model; Benchmarking; Binding Sites; Bioinformatics; Biological Models; Biotechnology; Boston; Cells; Classification; Collaborations; Collection; Complex; Computer Simulation; Data; Data Analyses; Data Quality; Data Set; Databases; Elements; Escherichia coli; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genome; Genome Mappings; Genomics; Gold; Grant; Growth; Institutes; International; Internet; Knowledge; Life; Link; Literature; Manuals; Maps; Metabolism; Methodology; Methods; Mexico; Modeling; Natural Language Processing; Network-based; Ontology; Operon; Organism; Outcome; Pathway interactions; Physiology; Process; Publications; Regulation; Regulon; Research; Science; Services; Sigma Factor; Signal Transduction; Small RNA; Structure; System; Systems Biology; Text; Transcription Initiation; Transcription Initiation Site; Transduction Gene; Universities; Work; base; biological research; data exchange; design; improved; interest; mutant; natural language; novel; pathogen; promoter; protein protein interaction; public health relevance; reconstruction; research study; sensor; simulation; text searching; tool; transcription factor

DESCRIPTION (provided by applicant): The Center for Genomic Sciences of the National Autonomous University of Mexico (UNAM) in Cuernavaca and a group of collaborators propose to further develop and enrich the RegulonDB database. RegulonDB contains the largest electronically-available regulatory network of any living organism, that of Escherichia coli K-12. In the project we will expand the design, implement computational and conceptual models, and generate annotations derived from original literature of the different components of the regulatory network. We will experimentally map promoters and transcription units under different conditions. This project expands a previous grant supporting RegulonDB. High quality manual curation is to be enriched beyond transcription initiation to include signal-transduction connecting sensing with regulation, as well as with natural language text processing tools. We propose to continue an exhaustive experimental mapping of all possible transcription initiation sites in the genome and to perform an exhaustive experimental identification of transcription units in different conditions. The core of RegulonDB (literature-based network and the graphic and browsing tools) will be linked and made accessible, as optional user selections, with high-throughput available experiments (microarrays and ChIP- chip) both as raw and pre-analyzed data, as well as with collections of computational predictions of all network elements (transcription factors, promoters, binding sites, operons, regulatory interactions). This will be based on track representations and compliant with international consortia normalized pathway exchange formats. The openness of RegulonDB data and internal structure will expand considerably, enhancing as well its availability to tools for analysis and representation. PUBLIC HEALTH RELEVANCE: RegulonDB is a gold standard both in its conceptual and computational design, as well as in the amount and quality of data gathered on the largest and best characterized regulatory network of a single organism. The improvements and expansion of RegulonDB may accelerate research in other bacterial models, including pathogens. RegulonDB has served as a benchmark for a variety of computational predictive tools for components of the network. Furthermore, E.coli is at the forefront in systems biology as a proof-of-concept biological model to develop new methodologies in bioinformatics, representation and simulation, to overcome challenges in order to model and understand the functioning of a whole cell.

描述（由申请人提供）：Cuernavaca国家自治大学（UNAM）的基因组科学中心，一组合作者建议进一步开发和丰富RegulondB数据库。 Regulondb包含任何生物体的最大的电子可用调节网络，即Escherichia Coli K-12。在项目中，我们将扩展设计，实施计算和概念模型，并生成源自监管网络不同组成部分的原始文献的注释。我们将在不同条件下实验绘制启动子和转录单元。该项目扩大了先前支持RegulondB的赠款。高质量的手动策划应超出转录启动，以包括连接与调节的传感以及自然语言文本处理工具的信号变形。我们建议继续对基因组中所有可能的转录起始位点进行详尽的实验映射，并在不同条件下对转录单元进行详尽的实验鉴定。 The core of RegulonDB (literature-based network and the graphic and browsing tools) will be linked and made accessible, as optional user selections, with high-throughput available experiments (microarrays and ChIP- chip) both as raw and pre-analyzed data, as well as with collections of computational predictions of all network elements (transcription factors, promoters, binding sites, operons, regulatory interactions).这将基于赛道表示形式，并符合国际财团标准化途径交换格式。 RegulondB数据和内部结构的开放性将大大扩展，并增强其对分析和表示工具的可用性。公共卫生相关性：RegulondB是其概念和计算设计的黄金标准，以及在单个生物体的最大，最佳特征的监管网络上收集的数据的数量和质量。在包括病原体在内的其他细菌模型中，RegulondB的改进和扩展可能会加速研究。 RegulondB已成为用于网络组件的各种计算预测工具的基准。此外，在系统生物学中，大肠杆菌是一种概念验证的生物学模型，以开发生物信息学，表示和仿真的新方法，以克服挑战以建模和了解整个细胞的功能。