) This first phase of this project will develop statistical methods for the design and analysis of gene expression microarray experiments based on statistical principles. Our experimental designs will allow a scientist to carry out classical (ANOVA style) experiments using microarray technology. Designed experiments offer quality control, normalization and a method of analysis that takes multiple sources of variation into account. New analysis tools will be developed based on the experimental designs and on our experience with array data generated in this phase of the project. We will establish the basic infrastructure, including informatics tools, for microarray analysis at the Jackson Laboratory. We will develop a detailed strategy, that is both robust and efficient, for a large scale survey of gene expression in tissue samples obtained from mouse models of mammary and ovarian cancers. The second phase of our project will involve carrying out this survey with the goal of classifying and charactering tumor types based on expression data. The expression data will be analyzed together with available information on the pathology of the tumor and the genetic background in which the tumor type arises. The ultimate goal of this project is to provide a sound statistical basis for the routine practice of expression profiling of mouse tumors. It is our premise that experimental design and design-based analysis tools are essential to obtaining high quality expression information at a reasonable cost.
