CAREER: New Technologies for Querying Pathway Databases

职业：查询路径数据库的新技术

• 批准号: 0845439
• 负责人: Tamer Kahveci
• 金额: $ 40万
• 依托单位: University of Florida
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-02-15 至 2015-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0845439&HistoricalAwards=false
• 关键词: CAREER; New; Technologies; Querying; Pathway

Unlike most bioinformatics data, such as DNA sequences and proteinstructures, pathways show the interactions of different bio-chemicalentities. Thus, each entity or subpathway can have a function in itspathway that the pathway can not realize without it. Formulating thesefunctions presents exciting computational challenges. This proposal develops algorithms for efficient and accuratecomputational analysis of pathways. The first step in achieving thisgoal is to build a mathematical model for functions of pathways andsubpathways. This proposal defines the function of a subpathway as itscontribution to the steady state of the entire pathway. Computing thiscontribution is a difficult problem especially for gene regulatorypathways. Existing methods can compute this for metabolic pathways,but they do not scale to even medium sized gene regulatorypathways. This proposal develops efficient methods for computingfunction.Finding the subpathway that has a desired function is a challengingproblem. There is no clear way of searching for subpathways withdesired functions using existing tools. This proposal developsefficient algorithms for searching subpathways with desired function.This proposal takes this one step further, and develops mathematicallysound algorithms for comparing two pathways so that the entities thatmap are functionally, homologically and topologically similar. Thisproposal also explores feature and reference-based index structuresfor biological pathway databases.Further information on the project can be found at the project webpage: http://bioinformatics.cise.ufl.edu/

与大多数生物信息学数据（例如DNA序列和蛋白质结构）不同，途径显示了不同生物化学性的相互作用。因此，每个实体或子路径都可以在其路径中具有一个功能，即没有它，这条路径就无法意识到。制定这些功能带来了令人兴奋的计算挑战。该提案开发了算法，以进行途径有效且准确的计算分析。实现这一目标的第一步是建立一个数学模型，以实现途径和subpathways的功能。该提案将子路口的功能定义为对整个途径的稳态贡献。计算此贡献是一个困难的问题，尤其是对于基因调节路径而言。 现有方法可以计算出代谢途径，但它们甚至不扩展到中等大小的基因调节路径。该建议开发了计算功能的有效方法。找到具有所需函数的子路口是一个挑战的问题。没有明确的方法可以使用现有工具搜索删除功能。该提案开发了用于搜索带有所需功能的子路口的算法。此提案将此提高了一步，并开发了数学上的算法，用于比较两种途径，以使映射在功能上，同源性和拓扑上相似。 此Proposs还探讨了生物途径数据库的功能和基于参考的索引结构。项目网页上的信息信息可以在项目网页上找到：http：//bioinformatics.cise.cise.ufl.edu/