Massive datasets such as gene expression profiles are accumulating along with the development of DNA microarray technologies. In this paper, we focus on mining biological relevant information such as typical expression patterns and the interconnections of gene networks from massive datasets. At first, the algorithm of a self-organizing map (SOM) was used to cluster gene expression data. Then, for the typical patterns extracted by the SOM, a three-layer artificial neural network (ANN) model was used to extract the relationships between the expression patterns. In order to evaluate the clustering analysis based on the SOM, biological and statistical indices were introduced. To validate the efficiency of the scheme proposed for extracting the relationships between the expression patterns with the ANN, a test dataset was created and used for the test. Finally, the interconnections of a typical pattern of early G1, late G1, S, G2, and M phases in a yeast cell cycle were extracted and visualized.