title: Differential Gene Expression (DEX) and Alternative Splicing Events (ASE) for Temporal Dynamic Processes Using HMMs and Hierarchical Bayesian Modeling Approaches.
abstract: In gene expression profile, data analysis pipeline is categorized into four levels, major downstream tasks, i.e., (1) identification of differential expression; (2) clustering co-expression patterns; (3) classification of subtypes of samples; and (4) detection of genetic regulatory networks, are performed posterior to preprocessing procedure such as normalization techniques. To be more specific, temporal dynamic gene expression data has its inherent feature, namely, two neighboring time points (previous and current state) are highly correlated with each other, compared to static expression data which samples are assumed as independent individuals. In this chapter, we demonstrate how HMMs and hierarchical Bayesian modeling methods capture the horizontal time dependency structures in time series expression profiles by focusing on the identification of differential expression. In addition, those differential expression genes and transcript variant isoforms over time detected in core prerequisite steps can be generally further applied in detection of genetic regulatory networks to comprehensively uncover dynamic repertoires in the aspects of system biology as the coupled framework.
authors.affiliation: Department of Computer Science and Statistics, Jeju National University, Jeju City, 690-756, South Korea. sshshoh1105@gmail.com.
authors.forename: Sunghee
authors.initials: S
authors.lastname: Oh
authors.affiliation: Department of Mathematical Science, University of Cincinnati, Cincinnati, OH, 45221-0025, USA.
authors.forename: Seongho
authors.initials: S
authors.lastname: Song
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic
keywords: Alternative splicing event; Differential expression; Genetic regulatory network; HMMs and hierarchical Bayesian modeling; Temporal dynamics; Time series expression profile