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Table 2 Functional analysis of HCV-HCC-associated dmRE in TCGA

From: DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma

RE type

RE location (hg19)a

Proximal gene symbol

Distance to proximal gene (bp)

Genomic region

Differential methylation analysis (HCV-HCC vs normal)

RE methylation vs gene expression correlation analysis

Differential gene expression analysis (HCV-HCC vs normal)

Directionally consistent

Mean difference

p value

Max. Correlationb

Min. p valueb

log2 fold change

p value

LINE-1

chr10:134875427–134876211

ADGRA1

25,296

Intergenic

− 0.331

6.97E−07

− 0.23

0.613

− 3.358

0.004

No

LINE-1

chr6:9810984–9817010

N/A c

N/Ac

Intergenic

− 0.203

1.23E−06

N/Ac

N/Ac

N/Ac

N/Ac

N/Ac

LINE-1

chr7:4388884–4389235

SDK1

80,252

Intergenic

− 0.382

1.08E−07

0.62

0.008

− 0.018

0.980

Yes

LINE-1

chr7:4085177–4085587

SDK1

0

Intronic

− 0.365

3.29E−06

0.33

0.161

− 0.018

0.980

Yes

LINE-1

chr7:157594780–157595648

PTPRN2

0

Intronic

− 0.385

4.40E−05

0.72

0.004

− 1.053

0.116

Yes

LINE-1

chr11:2499185–2499531

KCNQ1

0

Intronic

− 0.408

1.83E−05

0.53

0.034

1.343

0.076

No

LINE-1

chr5:8084329–8090357

MTRR

183,093

Intergenic

− 0.168

1.47E−05

−0.51

0.044

0.062

0.866

Yes

LINE-1

chr2:242938503–242938722

LINC01237

0

Intronic

− 0.337

1.18E−05

0.28

0.274

0.764

0.344

No

LINE-1

chr7:157318533–157319261

PTPRN2

12,488

Intergenic

− 0.443

2.19E−09

0.67

0.003

− 1.053

0.116

Yes

LINE-1

chr8:142852678–142853054

MROH5

335,347

Intergenic

− 0.409

2.99E−05

−0.54

0.269

0.573

0.737

Yes

LINE-1

chr8:143458657–143458848

TSNARE1

0

Intronic

0.107

2.73E−05

0.58

0.020

0.960

0.013

Yes

LINE-1

chr2:1166233–1166668

SNTG2

0

Intronic

− 0.276

1.44E−05

0.82

0.047

− 0.102

0.955

Yes

Alu

chr13:30062564–30062769

MTUS2

0

Intronic

− 0.275

9.85E−07

0.52

0.156

− 3.564

0.335

Yes

Alu

chrX:103294139–103294294

H2BFM

222

Promoterd

− 0.390

1.13E−06

N/Ae

N/Ae

N/Ae

N/Ae

N/Ae

Alu

chr6:31598686–31598816

PRRC2A

0

Intronic

0.137

2.90E−06

0.25

0.284

1.089

0.001

Yes

  1. aRanked by statistical significance, within LINE-1 and Alu, respectively
  2. bMaximum magnitude of correlation and minimum p values across the CpGs in the RE
  3. cNo proximal gene identified within 500 kbp
  4. dWithin 2000 bp upstream of the transcription start site
  5. eExtremely low expression across samples