Table 1.
The recurrently differentially expressed genes between matched primary tumors and PVTTs
| Gene | Function | PvT | Freq | FDR | EdgeR | OS | VI |
|---|---|---|---|---|---|---|---|
| DCN | Down | 11 | < 1e-05 | No | 0 | 1 | |
| CYP2E1 | Xenobiotics metabolism | Down | 8 | 8.75E-05 | No | 1 | 1 |
| LUM | Down | 8 | 8.75E-05 | No | 0 | 1 | |
| TNC | Focal adhesion | Up | 8 | < 1e-05 | No | 0 | 0 |
| TAT | AA metabolism | Down | 8 | 8.75E-05 | No | 2 | 3 |
| LAMA2 | Focal adhesion | Down | 8 | 8.75E-05 | Yes | 0 | 1 |
| SFRP4 | Down | 8 | 8.75E-05 | No | 0 | 0 | |
| CPS1 | AA metabolism | Down | 8 | 8.75E-05 | No | 1 | 3 |
| CYP3A4 | Xenobiotics metabolism | Down | 8 | 8.75E-05 | No | 1 | 3 |
| IGJ | Down | 7 | 1.44E-03 | No | 0 | 1 | |
| CYP2C8 | Xenobiotics metabolism | Down | 7 | 1.44E-03 | No | 0 | 3 |
| CYP1B1 | Xenobiotics metabolism | Down | 7 | 1.44E-03 | Yes | 0 | 0 |
| COLEC11 | Down | 7 | 1.44E-03 | No | 0 | 1 | |
| IGLL5 | Down | 7 | 1.44E-03 | Yes | 0 | 0 | |
| ASPN | Down | 7 | 1.44E-03 | No | 0 | 0 | |
| PDGFRA | Focal adhesion | Down | 7 | 1.44E-03 | No | 0 | 1 |
| ACTG2 | Up | 7 | 3.00E-04 | Yes | 0 | 0 | |
| INHBA | Down | 7 | 1.44E-03 | No | 0 | 0 | |
| HPD | AA metabolism | Down | 7 | 1.44E-03 | No | 1 | 1 |
| LAMC3 | Focal adhesion | Down | 7 | 1.44E-03 | Yes | 0 | 1 |
“PvT” denotes the direction of the differential expressions by comparing PVTTs to primary tumors; “Freq” denotes the number of patients with differentially expressed genes; “FDR” denotes the one-sided FDR calculated by permutation test; “EdgeR” denotes whether the gene is detected by EdgeR differential analysis (paired test, q-value < 0.1); “OS” denotes the number of datasets (two cohorts in total) in which the gene is significantly associated with overall survivals (KM test, p-value < 0.05); and, “VI” denotes the number of datasets (three cohorts in total) in which the gene is significantly associated with vascular invasion (ANOVA test, p-value < 0.05)