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Register a new userA 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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Haiyan Wu
Publication date
2007
fields
Mathematical Statistics
and research's language is
English
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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.
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Motivation: Time course data obtained from biological samples subject to specific treatments can be very useful for revealing complex and novel biological phenomena. Although an increasing number of time course microarray datasets becomes available, most of them contain few biological replicates and time points. So far there are few computational methods that can effectively reveal differentially expressed genes and their patterns in such data. Results: We have proposed a new two-step nonparametric statistical procedure, LRSA, to reveal differentially expressed genes and their expression trends in temporal microarray data. We have also employed external controls as a surrogate to estimate false discovery rates and thus to guide the discovery of differentially expressed genes. Our results showed that LRSA reveals substantially more differentially expressed genes and have much lower than two other methods, STEM and ANOVA, in both real data and the simulated data. Our computational results are confirmed using real-time PCRs. Contact: [email protected]
Complete understanding of the mechanisms regulating the proliferation and differentiation that takes place during human immune CD8+ T cell responses is still lacking. Human clinical data is usually limited to blood cell counts, yet the initiation of these responses occurs in the draining lymph nodes; antigen-specific effector and memory CD8+ T cells generated in the lymph nodes migrate to those tissues where they are required. We use approximate Bayesian computation with deterministic mathematical models of CD8+ T cell populations (naive, central memory, effector memory and effector) and yellow fever virus vaccine data to infer the dynamics of these CD8+ T cell populations in three spatial compartments: draining lymph nodes, circulation and skin. We have made use of the literature to obtain rates of division and death for human CD8+ T cell population subsets and thymic export rates. Under the decreasing potential hypothesis for differentiation during an immune response, we find that, as the number of T cell clonotypes driven to an immune response increases, there is a reduction in the number of divisions required to differentiate from a naive to an effector CD8+ T cell, supporting the division of labour hypothesis observed in murine studies. We have also considered the reverse differentiation scenario, the increasing potential hypothesis. The decreasing potential model is better supported by the yellow fever virus vaccine data.
Ethane is the most abundant non-methane hydrocarbon in the Earths atmosphere and an important precursor of tropospheric ozone through various chemical pathways. Ethane is also an indirect greenhouse gas (global warming potential), influencing the atmospheric lifetime of methane through the consumption of the hydroxyl radical (OH). Understanding the development of trends and identifying trend reversals in atmospheric ethane is therefore crucial. Our dataset consists of four series of daily ethane columns obtained from ground-based FTIR measurements. As many other decadal time series, our data are characterized by autocorrelation, heteroskedasticity, and seasonal effects. Additionally, missing observations due to instrument failure or unfavorable measurement conditions are common in such series. The goal of this paper is therefore to analyze trends in atmospheric ethane with statistical tools that correctly address these data features. We present selected methods designed for the analysis of time trends and trend reversals. We consider bootstrap inference on broken linear trends and smoothly varying nonlinear trends. In particular, for the broken trend model, we propose a bootstrap method for inference on the break location and the corresponding changes in slope. For the smooth trend model we construct simultaneous confidence bands around the nonparametrically estimated trend. Our autoregressive wild bootstrap approach, combined with a seasonal filter, is able to handle all issues mentioned above.
We introduce and analyze several aspects of a new model for cell differentiation. It assumes that differentiation of progenitor cells is a continuous process. From the mathematical point of view, it is based on partial differential equations of transport type. Specifically, it consists of a structured population equation with a nonlinear feedback loop. This models the signaling process due to cytokines, which regulate the differentiation and proliferation process. We compare the continuous model to its discrete counterpart, a multi-compartmental model of a discrete collection of cell subpopulations recently proposed by Marciniak-Czochra et al. in 2009 to investigate the dynamics of the hematopoietic system. We obtain uniform bounds for the solutions, characterize steady state solutions, and analyze their linearized stability. We show how persistence or extinction might occur according to values of parameters that characterize the stem cells self-renewal. We also perform numerical simulations and discuss the qualitative behavior of the continuous model vis a vis the discrete one.
Predicting equipment failure is important because it could improve availability and cut down the operating budget. Previous literature has attempted to model failure rate with bathtub-formed function, Weibull distribution, Bayesian network, or AHP. But these models perform well with a sufficient amount of data and could not incorporate the two salient characteristics; imbalanced category and sharing structure. Hierarchical model has the advantage of partial pooling. The proposed model is based on Bayesian hierarchical B-spline. Time series of the failure rate of 99 Republic of Korea Naval ships are modeled hierarchically, where each layer corresponds to ship engine, engine type, and engine archetype. As a result of the analysis, the suggested model predicted the failure rate of an entire lifetime accurately in multiple situational conditions, such as prior knowledge of the engine.
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