Modeling and analysis of gene expression arrays

Abstract

Gene expression arrays are a technology used to measure quantities of messenger ribonucleic acid (mRNA). Application of the technology involves a variety of physical processes beginning with the acquisition of mRNA samples and ending with the fluorescence imaging of a gene expression array. This thesis examines these physical processes, develops a mechanistic model, and derives the analysis procedure based on the model. Chief advantages of this approach are that it accounts for certain previously unexplained array phenomena and is based in a clear way on physical knowledge allowing non-arbitrary determination of both the probability that any given gene has altered expression ratio relative to a control as well as the magnitude of this induction or repression. We demonstrate its use on simulated and real array data, and show that a considerable amount of previously unrecognized information concerning gene expression differences is inherent in the array measurements.