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Table 1 CpG probes mapped in miRNA-coding genes differentially methylated in PTC compared to NT

From: Loss of DNA methylation is related to increased expression of miR-21 and miR-146b in papillary thyroid carcinoma

Probe (ID)

miRNA gene

Genomic functional distribution

CpG context

Internal data

TCGA data

Delta β

P

P adj.

Delta β

P

FDR

cg19019198

MIRLET7G

TSS200

 

− 0.36

< 1e-07

< 1e-07

− 0.49

< 1e-07

< 1e-07

cg07181702

MIR21

Body

 

− 0.19

< 1e-07

< 1e-07

− 0.20

< 1e-07

< 1e-07

cg04276626

MIR21

TSS200

 

− 0.18

< 1e-07

< 1e-07

− 0.16

< 1e-07

< 1e-07

cg02515217

MIR21

TSS200

 

− 0.17

< 1e-07

< 1e-07

− 0.16

< 1e-07

< 1e-07

cg15759721

MIR21

Body

 

− 0.17

< 1e-07

< 1e-07

− 0.14

< 1e-07

< 1e-07

cg04805065

MIR33B

TSS1500

Shore

− 0.25

< 1e-07

< 1e-07

− 0.29

< 1e-07

< 1e-07

cg09186408

MIR33B

TSS1500

Shore

− 0.20

< 1e-07

< 1e-07

− 0.23

< 1e-07

< 1e-07

cg19619576

MIR33B

TSS1500

Shelf

− 0.16

< 1e-07

1e-07

− 0.21

< 1e-07

< 1e-07

cg01243312

MIR128–1

Body

 

0.20

< 1e-07

< 1e-07

0.23

< 1e-07

< 1e-07

cg10734581

MIR134

TSS1500

 

− 0.19

< 1e-07

< 1e-07

NA

NA

NA

cg15857661

MIR146B

TSS200

Shelf

− 0.33

< 1e-07

< 1e-07

− 0.34

< 1e-07

< 1e-07

cg05858126

MIR146B

TSS200

Shelf

− 0.32

< 1e-07

< 1e-07

− 0.33

< 1e-07

< 1e-07

cg05251190

MIR146B

TSS200

Shelf

− 0.30

< 1e-07

< 1e-07

− 0.29

< 1e-07

< 1e-07

cg13442016

MIR146B

Body

Shelf

− 0.29

< 1e-07

< 1e-07

− 0.29

< 1e-07

< 1e-07

cg09701700

MIR146B

TSS1500

Shelf

− 0.20

< 1e-07

< 1e-07

− 0.19

< 1e-07

< 1e-07

cg13309012

MIR155

Body

 

− 0.30

< 1e-07

< 1e-07

− 0.30

< 1e-07

< 1e-07

cg13449535

MIR200B

TSS1500

Shore

− 0.25

< 1e-07

< 1e-07

− 0.37

< 1e-07

< 1e-07

cg14144728

MIR200B

TSS1500

Shore

− 0.23

< 1e-07

< 1e-07

− 0.21

< 1e-07

< 1e-07

cg08096702

MIR211

TSS1500

 

− 0.29

< 1e-07

< 1e-07

− 0.34

< 1e-07

< 1e-07

cg11721554

MIR377

TSS1500

Shelf

− 0.17

< 1e-07

< 1e-07

− 0.20

< 1e-07

< 1e-07

cg05138957

MIR377

TSS1500

Shelf

− 0.15

< 1e-07

< 1e-07

− 0.19

< 1e-07

< 1e-07

cg21513316

MIR410

Body

Island

− 0.16

< 1e-07

< 1e-07

− 0.14

< 1e-07

< 1e-07

cg20547131

MIR412

TSS1500

Shore

− 0.17

< 1e-07

< 1e-07

− 0.15

< 1e-07

< 1e-07

cg14910227

MIR495

Body

 

− 0.19

< 1e-07

< 1e-07

− 0.27

< 1e-07

< 1e-07

cg11978784

MIR512–1

TSS1500

 

− 0.17

< 1e-07

< 1e-07

NA

NA

NA

cg10583119

MIR518D

TSS1500

 

− 0.18

< 1e-07

< 1e-07

− 0.22

< 1e-07

< 1e-07

cg17670263

MIR520C

TSS1500

 

− 0.21

< 1e-07

1e-07

− 0.27

< 1e-07

< 1e-07

cg05865548

MIR543

TSS200

 

− 0.16

< 1e-07

< 1e-07

− 0.22

< 1e-07

< 1e-07

cg04522625

MIR548A2

Body

 

0.24

< 1e-07

< 1e-07

0.30

< 1e-07

< 1e-07

cg18697991

MIR548A2

Body

 

0.19

< 1e-07

< 1e-07

0.20

< 1e-07

< 1e-07

cg03221073

MIR548F1

Body

 

− 0.41

< 1e-07

< 1e-07

− 0.34

< 1e-07

< 1e-07

cg25874148

MIR548F5

Body

 

− 0.28

< 1e-07

< 1e-07

NA

NA

NA

cg01719718

MIR548F5

Body

 

− 0.17

< 1e-07

2e-07

− 0.18

< 1e-07

< 1e-07

cg05878887

MIR548G

Body

 

− 0.31

< 1e-07

< 1e-07

− 0.33

< 1e-07

< 1e-07

cg21175685

MIR548G

Body

 

− 0.31

< 1e-07

< 1e-07

− 0.24

< 1e-07

< 1e-07

cg02145866

MIR548G

Body

 

− 0.29

< 1e-07

< 1e-07

− 0.30

< 1e-07

< 1e-07

cg26664528

MIR548H4

Body

Shore

− 0.28

< 1e-07

< 1e-07

NA

NA

NA

cg11539052

MIR548N

Body

Shore

− 0.20

< 1e-07

< 1e-07

NA

NA

NA

cg05966699

MIR567

TSS1500

 

− 0.16

< 1e-07

< 1e-07

− 0.24

< 1e-07

< 1e-07

cg06277638

MIR570

TSS1500

 

− 0.17

< 1e-07

< 1e-07

NA

NA

NA

cg09031823

MIR575

TSS1500

 

− 0.17

< 1e-07

7e-04

− 0.25

< 1e-07

< 1e-07

cg18948646

MIR575

TSS200

 

− 0.16

< 1e-07

< 1e-07

− 0.13

< 1e-07

< 1e-07

cg26620021

MIR641

TSS1500

Shore

− 0.28

< 1e-07

< 1e-07

NA

NA

NA

cg11035122

MIR758

TSS1500

 

− 0.15

< 1e-07

2e-06

− 0.18

< 1e-07

< 1e-07

cg02558026

MIR762

TSS1500

Shore

− 0.20

< 1e-07

< 1e-07

− 0.24

< 1e-07

< 1e-07

cg13204193

MIR942

Body

 

0.19

< 1e-07

< 1e-07

NA

NA

NA

cg01940297

MIR1207

TSS1500

 

0.16

< 1e-07

3e-06

0.25

< 1e-07

< 1e-07

cg25037841

MIR1286

TSS1500

 

0.15

< 1e-07

< 1e-07

0.18

< 1e-07

< 1e-07

cg25591377

MIR1288

TSS1500

 

− 0.27

< 1e-07

< 1e-07

− 0.24

< 1e-07

< 1e-07

cg02746110

MIR1301

TSS1500

 

0.16

< 1e-07

4e-07

0.18

< 1e-07

< 1e-07

  1. NA probes not available in the TCGA processed data (level 3); P Adj Bonferroni P value; FDR false discovery ratio; TSS transcription start sites; Shelf, 2–4 kb from CpG island; Shore, until 2 kb from CpG island