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. Author manuscript; available in PMC: 2009 Oct 5.
Published in final edited form as: Mol Cancer Res. 2008 May;6(5):760–769. doi: 10.1158/1541-7786.MCR-07-0344

Figure 3. Genes Up-regulated in the Metastatic Derivatives from Set A Correlate with Metastatic Death in Human Melanoma Patients.

Figure 3

A. The 185 probe sets (150 genes; see text) were used as the template for the nearest template prediction (for details, see Materials and Methods). They include 99 up-regulated probe sets (indicated by an orange bar) and 86 down-regulated probe sets (indicated by a green bar). Expression values of the 185 probe sets were extracted from expression profiling data from human melanoma metastases and were used to calculate the distance of each sample from the template. The human melanoma metastases were separated into three classes based on their distance and FDR value. Class 1 metastases (red bar) express high levels of the up-regulated genes in the signature, FDR < 0.05; class 3 metastases (blue bar) express high levels of the down-regulated genes in the signature, FDR < 0.05; and class 2 metastases (grey bar) express intermediate levels of the signature genes, FDR > 0.05.

B. Kaplan-Meier survival curves were generated based on the correlation between the survival of patients and the classes of metastases they carry. The difference in survival probability between patients with the class 1 and class 3 metastases was found to be significant by a log-rank test. C. Similar analyses were performed as in A, but using expression data from primary human melanomas. The 185 probe sets (with the up-regulated ones indicated by an orange bar and down-regulated ones indicated by a green bar) separated the primary melanomas into three classes (red, grey and blue bars, respectively). Those melanomas that gave rise to metastases are labeled by black dots. Their Breslow thicknesses and Clark levels are labeled by colored hexagons and squares, respectively. The two extreme classes (class 1 and 3) of primary melanomas do not differ in their abilities to develop metastases (p = 0.224, Fisher’s exact test), or their Breslow thicknesses (p = 0.32 if the proportion of samples with thickness of less than 1 mm was compared between the two classes, Fisher’s exact test), or their Clark levels (p = 0.38 if the proportion of level III samples was compared between the two classes, Fisher’s exact test). They also did not differ significantly in survival probability (p = 0.106, log-rank test), possibly because of the small number of patients available for analysis (see Discussion).