In this paper, we discuss possible applications of virtual reality technologies, such as immersive projection technology (IPT), in the field of genome science, and propose cluster-oriented visualization that attaches importance to data separation of large gene data sets with multiple variables. Based on these strategies, we developed the cluster overlap distribution map (CDCM), which is a visualization methodology using IPT for pairwise comparison between cluster sets generated from different gene expression data sets. This methodology effectively provides the user with indications of gene clusters that are worth a close examination. In addition, by using the plate window manager system, which enables the user to manipulate existing 2D GUI applications in the virtual 3D space, we developed the virtual environment for the comprehensive analysis from providing the indications to further examination by referring to the database on Web sites. Our system was applied in the comparison between the gene expression data sets of hepatocellular carcinomas and hepatoblastomas, and the effectiveness of the system was confirmed.