Modern biology extensively deals with high throughput gene expression data. Although these datasets provide information about the expression of thousands of transcripts, the extraction of information desired by the researcher is a challenging task. Up to now, a variety of different analysis methods and tools have been developed. This book provides an overview of the mechanisms of gene regulation and discusses several of the expression data analysis methods based on the underlying model conceptions. On the basis of three different case studies, distinct analysis approaches are presented and comprehensive discussion of the results is provided.