Copula-Based Bayesian Model for Detecting Differential Gene Expression

Deoxyribonucleic acid, more commonly known as DNA, is a fundamental genetic material in all living organisms, containing thousands of genes, but only a subset exhibit differential expression and play a crucial role in diseases. Microarray technology has revolutionized the study of gene expression, with two primary types available for expression analysis: spotted cDNA arrays and oligonucleotide arrays. This research focuses on the statistical analysis of data from spotted cDNA microarrays. Numerous models have been developed to identify differentially expressed genes based on the red and green fluorescence intensities measured using these arrays. We propose a novel approach using a Gaussian copula model to characterize the joint distribution of red and green intensities, effectively capturing their dependence structure. Given the right-skewed nature of the intensity distributions, we model the marginal distributions using gamma distributions. Differentially expressed genes are identified using the Bayes estimate under our proposed copula framework. To evaluate the performance of our model, we conduct simulation studies to assess parameter estimation accuracy. Our results demonstrate that the proposed approach outperforms existing methods reported in the literature. Finally, we apply our model to Escherichia coli microarray data, illustrating its practical utility in gene expression analysis.