In recent years, relating gene expression to cancer development and treatment has received a lot of attention. Unfortunately, the availability of effective analysis tools lacks far behind the availability of data. In this paper, we present the Gene Expression Analyzer (GEA) for performing cluster analysis on gene expression data. In particular, the GEA is developed to support the reality that cluster analysis is typically a multi-step process. The underlying model of the GEA provides a set of algebraic operators for manipulating the data, as well as the intermediate results. Moreover, the GEA provides facilities to help the user to identify candidate genes for further clinical analysis. Last but not least, the GEA is optimized to handle the high dimensionality of gene expression data.