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Table 5 Hypomethylated and transcriptionally repressed genes ( n = 56) in HCC as compared to cancer-free tissue

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

Cell communication (8) a

Gene Name

P value

Coefficient

CRHBP

0.001

−5.0

DCN

0.027

−2.8

DLG2

0.035

−1.2

EMR1

0.009

−1.5

GPR128

0.002

−2.9

GRM8

0.004

−2.0

IGF1

0.046

−1.9

SPG20

0.006

−1.1

Immune response (9) a

Gene Name

P value

Coefficient

CLEC1B

0.002

−2.6

COLEC10

0.00002

−3.5

FCRL6

0.034

−1.1

FPR1

0.025

−1.8

IL1RL1

0.046

−1.6

LILRA5

0.028

−1.5

MARCO

0.0006

−3.2

NLRP12

0.003

−1.1

RAG1

0.022

−1.2

Transport (7) a

Gene Name

P value

Coefficient

AQP4

0.043

−1.1

EHD3

0.008

−2.4

LST-3TM12

0.021

−2.3

LYVE1

0.0002

−3.7

SLC38A4

0.038

−1.9

SLC6A19

0.018

−1.2

SYTL3

0.035

−1.2

Metabolic and cellular process (15) a

Gene Name

P value

Coefficient

DERA

0.016

−1.1

FBXL5

0.012

−1.1

FOLH1

0.029

−1.5

FRMD4B

0.02

−1.2

GALC

0.016

−1.3

GCNT2

0.005

−1.3

GLYATL1

0.029

−1.3

HEPACAM

0.019

−3.2

HSD11B1

0.023

−1.1

KLHL3

0.007

−1.9

NME5

0.017

−1.3

PBX1

0.012

−1.1

POU6F2

0.012

−1.2

RDH14

0.021

−1.3

TBXAS1

0.031

−1.5

Cell growth, cell cycle and apoptosis (6) a

Gene Name

P value

Coefficient

ABI3BP

0.01

−1.4

CNTN3

0.008

−1.6

MACF1

0.003

−1.1

PDE4DIP

0.001

−1.5

PTPN13

0.021

−1.9

TBRG1

0.018

−1.5

Miscellaneous (10) a

Gene Name

P value

Coefficient

C14orf105

0.013

−1.3

DOCK8

0.042

−1.4

ITLN1

0.016

−1.7

MBNL2

0.021

−1.9

NEBL

0.045

−1.1

PAMR1

0.01

−2.1

PLCXD3

0.038

−1.7

RNF217

0.009

−1.1

TMEM100

0.013

−1.5

TMEM133

0.001

−1.2

ZNF385B

0.035

−1.8

  1. aNumber of genes hypermethylated and transcriptionally repressed. Coefficient and P value refer to gene expression data.