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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.