Methodology article

Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration

Yulan Liang¹ and Arpad Kelemen²

¹  Department of Organizational Systems and Adult Health, University of Maryland, 655 W. Lombard Street, Baltimore, MD 21201-1579, USA

²  Department of Neurology, Buffalo Neuroimaging Analysis Center, The Jacobs Neurological Institute, University at Buffalo, The State University of New York, 100 High Street, Buffalo, NY 14203, USA

author email corresponding author email

BMC Bioinformatics 2008, 9:354doi:10.1186/1471-2105-9-354

Published:	28 August 2008

Abstract

Background

This paper addresses key biological problems and statistical issues in the analysis of large gene expression data sets that describe systemic temporal response cascades to therapeutic doses in multiple tissues such as liver, skeletal muscle, and kidney from the same animals. Affymetrix time course gene expression data U34A are obtained from three different tissues including kidney, liver and muscle. Our goal is not only to find the concordance of gene in different tissues, identify the common differentially expressed genes over time and also examine the reproducibility of the findings by integrating the results through meta analysis from multiple tissues in order to gain a significant increase in the power of detecting differentially expressed genes over time and to find the differential differences of three tissues responding to the drug.

Results and conclusion

Bayesian categorical model for estimating the proportion of the 'call' are used for pre-screening genes. Hierarchical Bayesian Mixture Model is further developed for the identifications of differentially expressed genes across time and dynamic clusters. Deviance information criterion is applied to determine the number of components for model comparisons and selections. Bayesian mixture model produces the gene-specific posterior probability of differential/non-differential expression and the 95% credible interval, which is the basis for our further Bayesian meta-inference. Meta-analysis is performed in order to identify commonly expressed genes from multiple tissues that may serve as ideal targets for novel treatment strategies and to integrate the results across separate studies. We have found the common expressed genes in the three tissues. However, the up/down/no regulations of these common genes are different at different time points. Moreover, the most differentially expressed genes were found in the liver, then in kidney, and then in muscle.