Bayesian Models for Gene Expression with Microarray Data

利用微阵列数据进行基因表达的贝叶斯模型

• 批准号: 7237216
• 负责人: Bani K Mallick
• 金额: $ 27.25万
• 依托单位: TEXAS A&M UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-06-10 至 2009-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7237216
• 关键词: Address; Algorithms; Base Sequence; Bayesian Method; Binding; Biological; Books; Class; Classification; Cluster Analysis; Code; Complex; Computer software; Computing Methodologies; Condition; DNA; DNA Microarray Chip; DNA Microarray format; Data; Data Analyses; Data Set; Dependency; Dimensions; Disease regression; Funding; Gene Cluster; Gene Expression; Genes; Genetic Models; Genomics; Goals; Grant; Home Page; Individual; Internet; Joints; Learning; Literature; Maps; Markov Chains; Markov chain Monte Carlo methodology; Measurement; Measures; Methods; Microarray Analysis; Modeling; Monte Carlo Method; Names; Nucleic acid sequencing; Numbers; Parents; Pattern; Performance; Phenotype; Pliability; Principal Investigator; Process; Property; Purpose; Range; Research; Sample Size; Sampling; Site; Space Models; Standards of Weights and Measures; Statistical Models; Techniques; Time; Tissue-Specific Gene Expression; Uncertainty; Weight; Work; Yang; base; cancer diagnosis; computer based statistical methods; density; experience; network models; novel; optimism; programs; response; simulation; teacher; tool; tumor

DESCRIPTION (provided by applicant): This project is concerned with parametric and semiparametric modeling of gene expression data. DNA microarrays and other high-throughput methods for analyzing complex nucleic acid sequences now make it possible to rapidly, efficiently and accurately measure the levels of many genes expressed in a biological sample. The main difficulty with microarray data analysis is that the sample size is very small when compared to the dimension of the problem (the number of genes). The number of genes for a single individual is usually in the thousands and there are few individuals in the data set. We propose several novel parametric Bayesian modeling approaches for gene selection, tumor classification, Bayesian networks, gene clustering and dimension reduction methods. Most of the existing methods are not model-based and thus are unable to address specific questions regarding formal assessment of uncertainties or assessment of the fit of a specific model. Also model-based approaches offer the potential for extension to more complex situations, e.g., probabilistic mixture modeling, handling missing data, etc. We will develop Bayesian hierarchical models for microarray data, which will accommodate several modeling factors flexibly at different levels. In several of the modeling frameworks, we will keep the dimension of the model space unknown to create added flexibility. It is impossible to get analytical answers in these flexible classes of models so simulation based Markov Chain Monte Carlo (MCMC) methodology with dimensional jumping algorithms will be used to derive the estimates (uncertainty distributions) of the unknown parameters.

描述（申请人提供）：本项目涉及基因表达数据的参数和半参数建模。DNA微阵列和其他用于分析复杂核酸序列的高通量方法现在使得快速、有效和准确地测量生物样品中表达的许多基因的水平成为可能。微阵列数据分析的主要困难在于，与问题的维度（基因数量）相比，样本量非常小。单个个体的基因数量通常是数千个，数据集中的个体很少。我们提出了几种新的参数贝叶斯建模方法的基因选择，肿瘤分类，贝叶斯网络，基因聚类和降维方法。大多数现有的方法都不是基于模型的，因此无法解决有关正式评估不确定性或评估特定模型的拟合度的具体问题。此外，基于模型的方法提供了扩展到更复杂情况的可能性，例如，我们将开发用于微阵列数据的贝叶斯分层模型，该模型将在不同水平上灵活地容纳几个建模因素。在几个建模框架中，我们将保持模型空间的维度未知，以增加灵活性。在这些灵活的模型类别中不可能得到分析答案，因此将使用基于模拟的马尔可夫链蒙特卡罗（MCMC）方法和维度跳跃算法来推导未知参数的估计值（不确定性分布）。