A statistical analysis of memory CD8 T cell differentiation: An application of a hierarchical state space model to a short time course microarray experiment
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Publication:2466472
DOI10.1214/07-AOAS118zbMATH Open1126.62110arXiv0712.1124MaRDI QIDQ2466472FDOQ2466472
Authors: Ming Yuan, Susan M. Kaech, M. Elizabeth Halloran, Hai-Yan Wu 
Publication date: 15 January 2008
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
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.
Full work available at URL: https://arxiv.org/abs/0712.1124
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Applications of statistics to biology and medical sciences; meta analysis (62P10) Medical applications (general) (92C50) Empirical decision procedures; empirical Bayes procedures (62C12)
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Cited In (6)
- Assessing multivariate predictors of financial market movements: A latent factor framework for ordinal data
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- Detecting T cell activation using a varying dimension Bayesian model
- A multiscale model of the CD8 T cell immune response structured by intracellular content
- Profiling the effects of short time-course cold ischemia on tumor protein phosphorylation using a Bayesian approach
- A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data
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