A STATISTICAL ANALYSIS OF MEMORY CD8 T CELL DIFFERENTIATION: AN APPLICATION OF A HIERARCHICAL STATE SPACE MODEL TO A SHORT TIME COURSE MICROARRAY EXPERIMENT

• 成果类型: Article
• 署名作者: Wu, Haiyan; Yuan, Ming; Kaech, Susan M.; Halloran, M. Elizabeth
• 署名单位: Emory University; Rollins School Public Health; Yale University; University System of Georgia; Georgia Institute of Technology; University of Washington; University of Washington Seattle; Fred Hutchinson Cancer Center; University of Washington; University of Washington Seattle
• 刊物名称: ANNALS OF APPLIED STATISTICS
• ISSN/ISSBN: 1932-6157
• DOI: 10.1214/07-AOAS118
• 发表日期: 2007
• 页码: 442-458
• 关键词: singular-value decomposition; False Discovery Rate; gene-expression; inference

摘要

CD8 T cells are specialized immune cells that play an important role ill the regulation of antiviral immune response and the generation of protective immunity. In this paper we investigate the differentiation of memory CD8 T cells ill the immune response using a short time course microarray experiment. structurally, this experiment is similar to many ill that it involves measurements taken oil independent samples, in one biological group, at a small number of irregularly spaced time points, and exhibiting patterns of temporal I patter nonstationarity. To analyze this CD8 T-cell experiment. we develop a hierarchical state space model so that we can: (1) detect temporally differentially expressed genes, (2) identify the direction of successive changes over time, and (3) assess the magnitude of successive changes over time, and (3) assess the magnitude hidden Markov models into our model to utilize the information embedded ill the time series and set up the proposed hierarchical state space model ill an empirical Bayes framework to utilize the population information from the large-scale data. Analysis of the CD8 T-cell experiment using the proposed model results in biologically meaningful findings. Temporal patterns involved ill the differentiation of memory CDs T cells are summarized separately and performance of the proposed model is illustrated in a simulation study.