Bayesian hierarchical modeling and selection of differentially expressed genes for the EST data.
Expressed sequence tag (EST) sequencing is a one-pass sequencing reading of cloned cDNAs derived from a certain tissue. The frequency of unique tags among different unbiased cDNA libraries is used to infer the relative expression level of each tag. In this article, we propose a hierarchical multinomial model with a nonlinear Dirichlet prior for the EST data with multiple libraries and multiple types of tissues. A novel hierarchical prior is developed and the properties of the proposed prior are examined. An efficient Markov chain Monte Carlo algorithm is developed for carrying out the posterior computation. We also propose a new selection criterion for detecting which genes are differentially expressed between two tissue types. Our new method with the new gene selection criterion is demonstrated via several simulations to have low false negative and false positive rates. A real EST data set is used to motivate and illustrate the proposed method.
Yu
Fang
F
Department of Biostatistics, University of Nebraska Medical Center, Omaha, Nebraska 68198-4350, USA.fangyu@unmc.edu
Chen
Ming-Hui
MH
Kuo
Lynn
L
Huang
Peng
P
Yang
Wanling
W
D000465:Algorithms; D001499:Bayes Theorem; D001699:Biometry / Q000379:methods; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D029968:Escherichia coli Proteins / Q000235:genetics*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D015233:Models, Statistical; D010363:Pattern Recognition, Automated / Q000379:methods
D029968:Escherichia coli Proteins