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Table 2 List of 35 cross-species conserved early HCC signature genes with qRT-PCR and independent human/rat early HCC validations overlaid

From: Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old

Gene Symbol 1

Description

Chromosomal Loci

P-value

qRT-PCR

Independent Validation Datasets.

     

Human

Rat

     

Chiang et al.

Boyault et al.

Liao et al.

Liu et al.

VIM*

vimentin

10p13

1.49E-16

DEa

NS

NS

NS

DEc

DCN

decorin

12q21.33

2.86E-15

DEb

DEc

DEc

DEc

DEc

EIF4EBP1*

eukaryotic translation initiation factor 4E binding protein 1

8p12

8.91E-15

NA

DEc

NS

NS

NS

AQP1

aquaporin 1 (channel-forming integral protein, 28 kDa)

7p14

1.15E-14

NA

NS

DEd

NS

NS

IMPA2

inositol(myo)-1(or 4)-monophosphatase 2

18p11.2

7.74E-14

NA

NS

DEd

NS

NS

FBN1

fibrillin 1

15q21.1

1.75E-12

NA

NS

NS

NS

NS

DCK*

deoxycytidine kinase

4q13.3-q21.1

4.22E-11

NA

DEc

 

DEc

NS

GJA1*

gap junction protein, alpha 1,43kDa (connexin 43)

6q21-q23.2

5.08E-11

DEa

NS

DEc

DEd

DEc

SP100*

SP100 nuclear antigen

2q37.1

6.95E-11

DEa

DEc

NS

NS

NS

SGCB*

sarcoglycan, beta (43kDa dystrophin-associated glycoprotein)

4q12

3.18E-10

NA

DEc

NS

NS

NS

FGFR2*

fibroblast growth factor receptor 2

10q26

1.15E-09

NA

NS

NS

DEd

NS

ABCC9

ATP-binding cassette, sub-family C (CFTR/MRP), member 9

12p12.1

1.75E-09

NA

DEc

NS

DEc

NS

MMP2*

matrix metallopeptidase 2

16q13-q21

1.22E-08

DEa

DEd

DEc

NS

NS

LGALS3BP*

lectin, galactoside-binding, soluble, 3 binding protein

17q25

4.29E-08

DEa

DEd

NS

NS

DEc

GSTA1*

glutathione S-transferase A1

6p12.1

5.16E-08

NA

NS

NS

NS

NS

NAT8

N-acetyltransferase 8

2p13.1-p12

3.20E-07

NA

DEc

DEd

DEd

NS

HMGB2*

high-mobility group box 2

4q31

3.34E-07

NA

DEc

DEd

DEd

NS

EXPH5

exophilin 5

11q22.3

6.15E-07

NA

DEc

NS

NS

NS

COL1A1*

collagen, type I, alpha 1

17q21.3-q22.1

7.62E-07

DEa

DEd

NS

NS

DEc

POLRMT

polymerase (RNA) mitochondrial (DNA directed)

19p13.3

7.95E-07

NA

DEc

NS

DEc

NS

AGPAT2

1-acylglycerol-3-phosphate O-acyltransferase 2

(lysophosphatidic acid acyltransferase, beta)

9q34.3

1.04E-06

NA

DEc

DEc

DEd

NS

CTBP2*

C-terminal binding protein 2

10q26.13

1.09E-06

NA

NS

NS

DEd

NS

PROM1

prominin 1

4p15.32

2.49E-06

NA

DEc

DEd

NS

NS

HPX*

hemopexin

11p15.5-p15.4

3.00E-06

NA

DEc

DEc

NS

NS

HEPH

hephaestin

Xq11-q12

3.15E-06

NA

NS

 

NS

DEc

HLA-DQA1*

major histocompatibility complex, class II, DQ alpha 1

6p21.3

2.68E-05

NA

DEd

DEd

NS

NS

COL5A2

collagen, type V, alpha 2

2q14-q32

3.88E-05

NA

DEd

NS

DEd

DEc

BIRC3

baculoviral IAP repeat-containing 3

11q22

6.19E-05

NA

DEd

NS

NS

NS

DPP4

dipeptidylpeptidase 4 (CD26, adenosine deaminase

complexing protein 2)

2q24.3

0.00034

DEa

DEc

NS

DEd

NS

AGL*

amylo-1, 6-glucosidase, 4-alpha-glucanotransferase

1p21

0.000426

NA

DEc

DEc

DEc

NS

PDZK1IP1

PDZK1 interacting protein 1

1p33

0.001118

NA

DEc

DEd

NS

NS

SRPX

sushi-repeat-containing protein, X-linked

Xp21.1

0.001189

NA

DEc

DEc

DEd

NS

IL13RA1

interleukin 13 receptor, alpha 1

Xq24

0.004051

NA

DEc

NS

DEc

NS

IGFBP3

insulin-like growth factor binding protein 3

7p13-p12

0.006904

DEa

DEc

DEc

DEc

DEc

PLN*

phospholamban

6q22.1

0.028062

NA

NS

NS

NS

NS

  1. 1 Genes with asterisk are also located in the chromosomal CNA regions.
  2. NA indicates genes for which qRT-PCR data are not available.
  3. aValidation was performed using whole blood of human early HCC patients (p < 0.05)
  4. bValidation was performed on rat early HCC tissues (p < 0.05); five additional rat genes that are not listed in Table 2 are also confirmed (Figure 6).
  5. cDifferentially expressed (p < 0.02 and fold change (FC) > 1.8); NS: Not significant
  6. dDifferentially expressed: FC > 1.8, but not statistically significant (p > 0.05)
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Molecular Cancer

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