Table 5. Differences in gene expression between M and NM MCTs measured by RT-qPCR.
| RT-qPCR | ||||||
|---|---|---|---|---|---|---|
| Gene symbol/ID. | Exon-level fold changea (NM/M) | No. NM MCTsb | No. M MCTsb | Fold changec (NM/M) | Spearman RCCd | p-valuee (Array) |
| CD9 | 2.25 (1.80) | 12 | 8 | 2.78 | 0.51 | 0.405 (0.090) |
| DSP | 19.08 (1.48) | 7 | 4 | 40.43 | 0.74 | 0.217 (0.152) |
| EGR1 | 3.66 (2.11) | 11 | 14 | 6.05 | 0.69 | 0.028 (0.050) |
| ENSCAFG-30560 | 2.05 (1.43) | 5 | 8 | 7.15 | 0.81 | 0.139 (0.213) |
| KRT10 | 23.43 (43.37) | 11 | 12 | 53.87 | 0.88 | 0.009 (0.017) |
| KRTAP4-4 | 2.10 (2.77) | 7 | 7 | 1.12 | 0.76 | 0.730 (0.208) |
| PERP | 7.38 (4.69) | 11 | 10 | 9.94 | 0.80 | 0.083 (0.041) |
| SBSN | 3.49 (2.62) | 10 | 6 | 14.77 | 0.81 | 0.140 (0.115) |
| SNORD93 | 0.25 (0.39) | 12 | 16 | 0.37 | 0.50 | 0.196 (0.258) |
aFold change differences in expression between 18 M and 16 NM MCTs determined by microarray—Ratio of median expression values for the Exon probe set upon which RT-qPCR assay design was based. In parenthesis are the fold change differences calculated when only the microarray-derived expression values of MCTs that yielded valid Cq values in RT-qPCR assay were considered.
bThe numbers of NM and M MCTs represent the numbers of samples for which valid Cq (Cq <35; Cq SD<0.5) measurements were obtained. ‘Non-valid’ Cq values were attributable to: Cq <35 or ‘undetermined’ and Cq SD>0.5.
cFold change determined by RT-qPCR assay.
dThe Spearman rank correlation coefficient (RCC) indicates the extent of the concordance between the expression values for individual MCT assayed by microarray and RT-qPCR, respectively.
eThe statistical significance of the RT-qPCR measured differences in expression between the NM and M MCTs determined by t-test. The statistical significance of the differences between the microarray-derived gene-level expression values measured for the same MCTs is shown in parenthesis.