Gene expression analysis of the different GCT subgroups. (A) A multidimensional scaling (MDS) plot containing the differentially expressed genes (690 probe sets, q < 0.001). Each spot represents a single array. (B) A comparison of the transcriptome traits between ESCs and NGMGCTs by principal component analysis (PCA). (C) Relationships between ESCs, germinomas and NGMGCTs. Average linkage Euclidean distances between the tissues and ESC were calculated using genes distinguishing the filtrated 690-probe set. The confidence limits shown represent the standard error. (D) A heat map shows genes enriched in the ESCs and in the different prognostic groups (q < 0.001). (E-F) Real-time PCR validation of the microarray data. Mean expression levels of the examined genes were compared to that of the GAPDH control. Each bar represents a different individual (F). The genes' array hybridization signals are also shown (E).