We analyzed gene expression profiles of five tumor cell lines (NB2a, NB41A3, C1300N18, BC3H1, and Neuro2a) derived from a category of nervous system using our originally developed cell surface marker DNA microarray in order to search for tumor-specific cell surface markers common to these cells. To visualize the expression patterns and to extract candidate genes of interest based on the expression profiles of several cell lines, we employed the clustering procedure of spherical self-organizing-map. As the result, three candidates of tumor-specific cell surface markers were picked up when the expression profiles were compared with that from normal brain tissue. RT-qPCR showed the expression of these genes was higher in tumor cells than in normal brain. Here we demonstrated the spherical self-organizing-map analysis should be useful to identify the candidates of cell surface markers common and specific to the group of cells or tissues of interest.