Open Access
December 2007 A statistical analysis of memory CD8 T cell differentiation: An application of a hierarchical state space model to a short time course microarray experiment
Haiyan Wu, Ming Yuan, Susan M. Kaech, M. Elizabeth Halloran
Ann. Appl. Stat. 1(2): 442-458 (December 2007). DOI: 10.1214/07-AOAS118

Abstract

CD8 T cells are specialized immune cells that play an important role in the regulation of antiviral immune response and the generation of protective immunity. In this paper we investigate the differentiation of memory CD8 T cells in the immune response using a short time course microarray experiment. Structurally, this experiment is similar to many in that it involves measurements taken on independent samples, in one biological group, at a small number of irregularly spaced time points, and exhibiting patterns of temporal 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. We incorporate hidden Markov models into our model to utilize the information embedded in the time series and set up the proposed hierarchical state space model in 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 in the differentiation of memory CD8 T cells are summarized separately and performance of the proposed model is illustrated in a simulation study.

Citation

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Haiyan Wu. Ming Yuan. Susan M. Kaech. M. Elizabeth Halloran. "A statistical analysis of memory CD8 T cell differentiation: An application of a hierarchical state space model to a short time course microarray experiment." Ann. Appl. Stat. 1 (2) 442 - 458, December 2007. https://doi.org/10.1214/07-AOAS118

Information

Published: December 2007
First available in Project Euclid: 30 November 2007

zbMATH: 1126.62110
MathSciNet: MR2415750
Digital Object Identifier: 10.1214/07-AOAS118

Keywords: Empirical Bayes , gene expression profiles , Hidden Markov model , microarrays , time course

Rights: Copyright © 2007 Institute of Mathematical Statistics

Vol.1 • No. 2 • December 2007
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