A cancer-specific transcriptional signature in human neoplasia
J. Clin. Invest. Francesco Nicassio, et al. 115:3015 doi:10.1172/JCI24862 [Go to this article.]

Figure 3
Class D genes in human tumors. (A) The overexpression of class D genes was tested by ISH on TMAs. The color code indicates the percentage of tumors in which overexpression was detected (actual numbers are reported in Supplemental Table 10). White, 0–20%; blue, 21–40%; green, 41–60%; orange, 61–80%; red, 81–100%. In almost all cases (with the exception of TRPC4AP and SF3B1 in normal colon; see Figure 4), normal counterparts (not reported here) showed low or undetectable levels of expression (≤ 1 on our scale; see Methods). Asterisks mark significant values (P < 0.05) of overexpression in tumors vs. normal counterparts. In some cases (uterus, melanoma [melan.], brain), statistical analysis could not be performed due to lack of normal tissues (see Supplemental Table 10 for further details). Eight other genes (from classes A–C, LBR, XTP1, MGC22679, K1594, C3orf4, CML66, K0648, and FLJ37562) showed no overexpression (not shown). Two additional class B genes (Np95 and Nasp) showed elevated mRNA levels in both tumors and proliferating cells of the normal counterparts, thus not fulfilling the criteria for overexpression (see text). (B) Examples of data reported in A. N, normal tissue; T, tumor. Top row, bright fields (histology); bottom row, dark fields (transcripts appear as bright dots). Original magnification, ×10. (C) Tumor and normal samples from colon and breast carcinoma patients were analyzed for levels of expression of SKIN by ISH (black bars) and Q–RT-PCR (white bars), respectively. Q–RT-PCR data are normalized to colon case 1N (assumed as 1.0). Data show good correlation between the 2 methods.