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A web platform for integrative genomic analysis in aging

用于衰老综合基因组分析的网络平台

基本信息

批准号：
7575726
负责人：
XIANGHONG Jasmine ZHOU
金额：
$ 16.71万
依托单位：
UNIVERSITY OF SOUTHERN CALIFORNIA
依托单位国家：
美国
项目类别：
财政年份：
2008
资助国家：
美国
起止时间：
2008-03-01 至 2011-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7575726
关键词：
Address Age Aging Ally Animal Model Atlases Bioinformatics Biological Biological Process Caenorhabditis elegans Cell Differentiation process Chronic Disease Communities Data Data Set Data Sources Databases Deposition Development Gap Junctions Gene Expression Genes Genetic Genome Genomics Human Inflammatory Internet Knowledge Laboratories Link Literature Malignant Neoplasms Measurement Measures Methods Microarray Analysis Mining Modeling Mus Organism Pathway interactions Pattern Phase Rattus Recurrence Reporting Research Resources Saccharomyces cerevisiae Signal Transduction System Tissues Transcription Regulation Pathway Transcriptional Regulation Vascular Diseases Work Yeasts age related aging gene base data integration data sharing design fly genome sequencing high throughput technology improved novel protein protein interaction research study tool user-friendly web interface

项目摘要

DESCRIPTION (provided by applicant): The recent development of high-throughput technologies generated enormous genomic data to understand the genetic basis of aging. For example, more than eighty microarray studies have directly addressed aging-related expression patterns in diverse model organisms and under different conditions. However, efficient exploitation of this vast amount of microarray data is frustrated by the lack of bioinformatics resources to enable convenient cross-laboratory searches of primary array signals. We have develop the web-database Gene Aging Nexus (GAN) freely accessible to the biogerontological-geriatric research community to query/analyze/visualize various aging-related genomic data sources, in particular, microarray data. In this proposal, we will continue the development of GAN. In particular, (1) We will expand the central web database for aging microarray data of six species: human (H. sapiens), rat (R. norvegicus), mouse (M. musculus), `fly' (D. melanogaster), `worm' (C. elegans), and yeast (S. cerevisiae). (2) We will implement a set of novel tools for cross-platform microarray data integration and analysis, and also implement useful methods reported in the literature. (3) We will incorporate other genomic data sources, such as biological pathways, transcription regulation, protein-protein interactions, genome sequences, and literature knowledge. By integrating such data, users will be able to better understand and interpret the results derived from array analysis, to assign unknown genes to aging-related pathways, and to predict transcriptional regulation. GAN could help launch the next phase of evaluating possible universals in aging-related gene expression in tissues of diverse organisms. The construction of the GAN platform and the associated analysis of a large number of public aging genomic data could constitute one of the largest bioinformatics undertakings in aging research. GAN could help launch the next phase of evaluating possible universals in aging-related gene expression in tissues of diverse organisms, and facilitates the systems understanding of aging.

描述(申请人提供)：高通量技术的最新发展产生了大量的基因组数据，以了解衰老的遗传基础。例如，80多项微阵列研究直接研究了不同模式生物在不同条件下与衰老相关的表达模式。然而，由于缺乏生物信息学资源来方便地跨实验室搜索初级阵列信号，阻碍了对这些海量微阵列数据的有效利用。我们已经开发了生物老年学-老年学研究社区免费访问的网络数据库基因老化关联(GAN)，以查询/分析/可视化各种与衰老相关的基因组数据源，特别是微阵列数据。在这份提案中，我们将继续发展GaN。具体地说，(1)我们将扩大用于六个物种的老化微阵列数据的中央网络数据库：人(智人)、大鼠(褐家鼠)、小鼠(肌肉分支杆菌)、苍蝇(黑腹隐翅虫)、蠕虫(线虫)和酵母(酿酒酵母)。(2)我们将实现一套新的跨平台微阵列数据集成和分析工具，并实现文献中报告的有用方法。(3)我们将纳入其他基因组数据来源，如生物途径、转录调控、蛋白质-蛋白质相互作用、基因组序列和文献知识。通过整合这些数据，用户将能够更好地理解和解释来自阵列分析的结果，将未知基因分配给与衰老相关的途径，并预测转录调控。GAN可以帮助启动下一阶段评估不同生物体组织中与衰老相关的基因表达的可能共性。 GAN平台的构建和对大量公开的衰老基因组数据的关联分析可能构成衰老研究中最大的生物信息学事业之一。GAN可以帮助启动下一阶段评估不同生物组织中与衰老相关的基因表达的可能共性，并促进对衰老的系统理解。