Bayesian finite Markov mixture model for temporal multi-tissue polygenic patterns.
Finite mixture models can provide the insights about behavioral patterns as a source of heterogeneity of the various dynamics of time course gene expression data by reducing the high dimensionality and making clear the major components of the underlying structure of the data in terms of the unobservable latent variables. The latent structure of the dynamic transition process of gene expression changes over time can be represented by Markov processes. This paper addresses key problems in the analysis of large gene expression data sets that describe systemic temporal response cascades and dynamic changes to therapeutic doses in multiple tissues, such as liver, skeletal muscle, and kidney from the same animals. Bayesian Finite Markov Mixture Model with a Dirichlet Prior is developed for the identifications of differentially expressed time related genes and dynamic clusters. Deviance information criterion is applied to determine the number of components for model comparisons and selections. The proposed Bayesian models are applied to multiple tissue polygenetic temporal gene expression data and compared to a Bayesian model-based clustering method, named CAGED. Results show that our proposed Bayesian Finite Markov Mixture model can well capture the dynamic changes and patterns for irregular complex temporal data.
Liang
Yulan
Y
Department of Organizational Systems and Adult Health, University of Maryland, Baltimore, 21201, USA. ylian001@umaryland.edu
Kelemen
Arpad
A
D000465:Algorithms; D001499:Bayes Theorem; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D008390:Markov Chains; D008957:Models, Genetic; D015233:Models, Statistical; D020412:Multifactorial Inheritance / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D020543:Proteome / Q000032:analysis; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D020543:Proteome