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Table 1 The recurrently differentially expressed genes between matched primary tumors and PVTTs

From: Integrative molecular analysis of metastatic hepatocellular carcinoma

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
  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)