Bayesian hierarchical modeling for time course microarray experiments.
Time course microarray experiments designed to characterize the dynamic regulation of gene expression in biological systems are becoming increasingly important. One critical issue that arises when examining time course microarray data is the identification of genes that show different temporal expression patterns among biological conditions. Here we propose a Bayesian hierarchical model to incorporate important experimental factors and to account for correlated gene expression measurements over time and over different genes. A new gene selection algorithm is also presented with the model to simultaneously identify genes that show changes in expression among biological conditions, in response to time and other experimental factors of interest. The algorithm performs well in terms of the false positive and false negative rates in simulation studies. The methodology is applied to a mouse model time course experiment to correlate temporal changes in azoxymethane-induced gene expression profiles with colorectal cancer susceptibility.
Chi
Yueh-Yun
YY
Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA. yychi@u.washington.edu
Ibrahim
Joseph G
JG
Bissahoyo
Anika
A
Threadgill
David W
DW
D000465:Algorithms; D000818:Animals; D001397:Azoxymethane / Q000633:toxicity; D001499:Bayes Theorem; D001699:Biometry; D015179:Colorectal Neoplasms / Q000139:chemically induced / Q000235:genetics; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D020022:Genetic Predisposition to Disease; D051379:Mice; D008815:Mice, Inbred Strains; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D013045:Species Specificity; D013997:Time Factors
D001397:Azoxymethane