Skip to main content

Table 2 Hypermethylated and transcriptionally repressed genes ( n = 159) in HCC as compared to cancer-free tissue

From: DNA methylation and gene expression profiles show novel regulatory pathways in hepatocellular carcinoma

Cell communication (17) a
Gene Name P value Coefficient Gene Name P value Coefficient Gene Name P value Coefficient
AKAP2 0.014 −1.5 INHBC 0.003 −1.4 RND3 0.002 −2.3
AMHR2 0.019 −1.4 MORN4 0.025 −1.2 SH3D19 0.004 −1.2
BZRAP1 0.039 −1.0 OLFML3 0.015 −2.3 SORBS2 0.013 −1.1
C1orf168 0.009 −1.5 PDE2A 0.011 −1.7 SUCNR1 0.006 −1.8
CLDN1 0.003 −1.0 PPL 0.01 −1.6 VNN1 0.031 −1.5
FES 0.00001 −1.5 RIC3 0.004 −1.8    
Immune response (23) a
Gene Name P value Coefficient Gene Name P value Coefficient Gene Name P value Coefficient
ANTXR2 0.012 −1.4 CFI 0.009 −1.0 KLKB1 0.007 −1.8
BLNK 0.002 −1.0 CFP 0.00002 −3.3 LILRA1 0.007 −1.2
C1QTNF1 0.035 −2.3 FCGR2B 0.047 −1.2 MBL2 0.046 −1.9
C1RL 0.016 −1.0 FCN2 0.00001 −3.7 MEFV 0.01 −1.4
C5AR1 0.037 −1.1 HAMP 0.01 −3.4 PGLYRP2 0.001 −1.9
CCL14 0.029 −1.5 IL13RA2 0.00001 −3.8 TINAGL1 0.043 −1.3
CCL15 0.029 −1.5 IL1B 0.005 −1.8 VSIG4 0.025 −2.4
CD302 0.003 −1.2 IL1RN 0.007 −1.1    
Transport (19) a
Gene Name P value Coefficient Gene Name P value Coefficient Gene Name P value Coefficient
ANXA8 0.043 −2.4 SLC10A1 0.019 −2.2 SLC5A1 0.012 −3.2
APOA5 0.004 −1.7 SLC22A1 0.002 −2.1 SLC6A12 0.007 −1.7
APOL6 0.005 −1.5 SLC22A10 0.009 −2.5 SLCO1B3 0.012 −3.7
AQP7 0.041 −1.0 SLC25A25 0.045 −1.3 SLCO2B1 0.001 −1.4
CETP 0.00001 −3.2 SLC25A47 0.011 −2.0 TRPV4 0.005 −2.1
MIP 0.006 −1.0 SLC45A3 0.012 −1.2    
RGN 0.009 −1.7 SLC47A1 0.033 −1.2    
Metabolic and cellular process (43) a
Gene Name P value Coefficient Gene Name P value Coefficient Gene Name P value Coefficient
ACADS 0.002 −1.3 FBXO3 0.004 −1.3 MOGAT2 0.00001 −3.2
ACSM5 0.026 −1.0 FMO3 0.019 −1.0 OAT 0.046 −2.0
AGMO 0.028 −1.3 GLUD2 0.004 −1.3 PLIN 0.012 −1.8
AMDHD1 0.048 −1.1 GPT 0.009 −1.0 PSD4 0.002 −1.2
ANK2 0.019 −1.0 GYS2 0.005 −3.0 TBXA2R 0.0004 −1.3
ANK3 0.026 −1.8 HGFAC 0.033 −3.1 UROC1 0.014 −2.5
ARSD 0.022 −1.4 HK3 0.003 −1.3 Retinol metabolism   
ATP11C 0.047 −1.0 HOGA1 0.002 −1.8 ADH1A 0.021 −1.4
BCO2 0.007 −3.1 IDO2 0.002 −3.7 ADH1B 0.021 −1.4
CES4A 0.023 −1.2 INMT 0.021 −1.2 ADH6 0.016 −1.9
CHST9 0.026 −1.5 IYD 0.003 −1.8 CYP3A43 0.027 −2.2
CPN1 0.014 −1.1 KDM5D 0.048 −1.5 CYP4A22 0.02 −1.1
CYP8B1 0.005 −2.7 LCAT 0.001 −1.8 RDH16 0.024 −1.4
DSE 0.022 −1.3 LDHD 0.018 −1.1 One-carbon metabolism   
EPHX2 0.025 −1.1 LPAL2 0.003 −1.4 SHMT1 0.003 −1.1
Cell growth, cell cycle and apoptosis (26) a
Gene Name P value Coefficient Gene Name P value Coefficient Gene Name P value Coefficient
ADORA3 0.014 −1.9 GDF2 0.00002 −2.7 TBX15 0.019 −1.7
AGTR1 0.006 −1.5 JDP2 0.007 −1.1 TNFRSF10D 0.025 −1.2
AR 0.038 −1.4 MAP2K3 0.007 −1.1 ZBED1 0.003 −1.1
AXL 0.049 −1.5 NAP1L5 0.004 −1.1 Candidate tumor-suppressor genes   
CAT 0.006 −1.1 NR4A1 0.043 −1.3 FAM107A 0.018 −1.3
DBH 0.002 −2.7 NUGGC 0.001 −1.8 IGFALS 0.00005 −3.2
DMD 0.043 −1.2 PTH1R 0.006 −2.5 MT1G 0.002 −2.8
ESR1 0.002 −3.0 PTPN3 0.001 −1.2 MT1H 0.004 −1.6
FGD4 0.01 −1.1 SMAD6 0.001 −1.3 RNF180 0.021 −1.2
Miscellaneous (31) a
Gene Name P value Coefficient Gene Name P value Coefficient Gene Name P value Coefficient
ADAMTSL2 0.04 −2.1 FAM13A 0.037 −1.6 PID1 0.019 −1.1
ALPL 0.003 −1.4 FAM65C 0.001 −1.4 PRSS53 0.026 −1.1
ANKRD55 0.001 −1.6 FAM83F 0.002 −1.4 SMOC1 0.015 −1.2
C10orf26 0.0001 −1.3 FXYD7 0.021 −1.1 SPATA18 0.005 −2.6
C10orf58 0.01 −1.2 HAPLN4 0.027 −1.6 SYNE1 0.021 −1.1
C17orf91 0.003 −1.2 INS-IGF2 0.0002 −4.2 TCTEX1D1 0.023 −1.3
C21orf84 0.04 −1.6 LINC00574 0.008 −1.1 TMEM125 0.039 −1.3
CCDC68 0.002 −1.6 LOC339240 0.014 −1.9 TMEM26 0.025 −1.2
CILP 0.0001 −2.1 LRRC25 0.039 −1.3 UNC93A 0.04 −1.2
DNALI1 0.003 −1.8 MYO15A 0.007 −1.2 WDR66 0.0001 −2.1
EXPH5 0.017 −2.3       
  1. aNumber of genes hypermethylated and transcriptionally repressed. Coefficient and P value refer to gene expression data.