Table VII.
Validation results using 28 PNI and 22 non-PNI tumors in the GSE102238 dataset.
| A, Top 10 DEGs (upregulated and downregulated) | ||
|---|---|---|
| Gene | FC | P-value |
| Upregulated DEGs | ||
| BNIP3 | 1.063 | 0.805 |
| EFEMP1 | 1.160 | 0.493 |
| GNB4 | 0.897 | 0.481 |
| NETO2 | 1.047 | 0.787 |
| LY75 | 0.880 | 0.414 |
| TSHZ3 | 1.212 | 0.282 |
| LIMS3 | N/A | N/A |
| TMSB15B | 1.118 | 0.486 |
| NAP1L5 | 1.116 | 0.400 |
| CLDN10 | 1.067 | 0.837 |
| Downregulated DEGs | ||
| SPON1 | 1.339 | 0.329 |
| CDH11 | 1.030 | 0.891 |
| SDPR | 1.169 | 0.485 |
| SOSTDC1 | 1.416 | 0.309 |
| LUM | 1.092 | 0.573 |
| IL1B | 0.851 | 0.524 |
| ESM1 | 1.141 | 0.667 |
| CCL20 | 0.730 | 0.406 |
| SULF2 | 0.996 | 0.978 |
| PDE4B | 0.763 | 0.188 |
| B, DEGs from KEGG pathways | ||
| Gene | FC | P-value |
| Vasopressin-regulated water reabsorption (upregulated) | ||
| DYNC1I1 | 1.081 | 0.584 |
| CREB5 | 1.059 | 0.708 |
| DYNC2H1 | 1.051 | 0.577 |
| PPAR signaling pathway (downregulated) | ||
| MMP1 | 0.583 | 0.172 |
| PCK1 | 0.922 | 0.830 |
| FABP3 | 0.870 | 0.368 |
| CD36 | 0.949 | 0.865 |
| ACOX2 | 1.053 | 0.509 |
| Pathways in cancer (downregulated) | ||
| CXCL12 | 1.061 | 0.794 |
| GNGT1 | 1.479 | 0.266 |
| FZD4 | 1.078 | 0.694 |
| GLI1 | 1.349 | 0.233 |
| FGFR1 | 1.196 | 0.243 |
| AR | 1.342 | 0.076 |
| FLT3 | 1.002 | 0.990 |
| IGF1 | 0.902 | 0.760 |
| CTNNA2 | 0.888 | 0.049a |
| GNG4 | 1.094 | 0.619 |
| FGF2 | 1.451 | 0.038a |
| C, Hub genes | ||
| Genes | FC | P-value |
| FGF2 | 1.451 | 0.038a |
| GLI1 | 1.349 | 0.233 |
| NPSR1 | 0.942 | 0.914 |
| CCR5 | 1.012 | 0.957 |
| PDE4D | 0.919 | 0.664 |
| TEK | 0.966 | 0.817 |
| FGFR1 | 1.196 | 0.243 |
| PGR | 1.237 | 0.239 |
| TNS1 | 1.275 | 0.074 |
| MAPT | 1.316 | 0.082 |
| AR | 1.342 | 0.076 |
| FLT3 | 1.002 | 0.990 |
| GNB4 | 0.897 | 0.481 |
| UBE2E1 | 0.997 | 0.974 |
| WWTR1 | 1.210 | 0.114 |
| TGFB2 | 1.262 | 0.304 |
| PRKG1 | 1.138 | 0.377 |
| SNCA | 1.012 | 0.944 |
| ITPR1 | 0.986 | 0.911 |
| MITF | 0.946 | 0.598 |
a
P<0.05. PNI, perineural invasion; DEGs, differentially expressed genes; FC, fold-change; Kyoto Encyclopedia of Genes and Genomes.