Table 2 Top 10 CpG sites showing the largest fold change between patients and controls.

From: Longitudinal genome-wide DNA methylation changes in response to kidney failure replacement therapy

 

Gene symbol

Probe no.

PFDR

Fold change

Controls vs dialysis baseline

D2HGDH

cg05385718

3.9 × 10–4

0.003

CDK6

cg06688763

4.1 × 10–4

0.044

AGAP3

cg25417842

4.1 × 10–3

0.045

PNKD

cg22712983

1.4 × 10–3

0.049

HIVEP3

cg12666727

2.1 × 10–4

0.05

HSDL1

cg08965527

1.0 × 10–4

34.8

RNASEH2C

cg25294185

1.2 × 10–4

36.3

ZNF562

cg21610904

3.6 × 10–3

39.9

CSGALNACT2

cg26674752

1.1 × 10–4

71.3

COL6A3

cg23813394

7.8 × 10–3

776.2

Controls vs dialysis 12 months

D2HGDH

cg05385718

8.1 × 10–3

0.007

PNKD

cg22712983

2.5 × 10–3

0.04

EID2

cg11976736

5.5 × 10–3

0.053

AGAP3

cg07429146

7.2 × 10–3

0.068

ETS1

cg24065451

8.7 × 10–4

0.076

MRFAP1

cg24475210

7.1 × 10–4

39

GBX1

cg04553410

6.8 × 10–4

41.9

RNASEH2C

cg25294185

3.3 × 10–4

44.7

ZNF224

cg26649251

1.4 × 10–4

83.2

cg12031275

7.4 × 10–3

288.5

Controls vs KTx baseline

TTC15

cg00257789

6.5 × 10–3

0.004

HLA-DRB5

cg25372449

4.8 × 10–3

0.01

PNKD

cg22712983

6.4 × 10–6

0.022

PRKAG2

cg06436185

1.4 × 10–6

0.022

FXYD2

cg01142676

1.8 × 10–6

0.027

BCL11B

cg16452866

2.4 × 10–6

35.7

NOSIP

cg21292909

3.3 × 10–7

38.4

IQSEC1

cg26692003

4.4 × 10–7

41.9

DGKA

cg07679948

3.6 × 10–6

45.2

RARG

cg13937905

4.9 × 10–6

54.3

Controls vs KTx 12 months

SSH3

cg22632840

1.5 × 10–4

0.044

cg13985485

3.5 × 10–3

0.054

cg11799593

5.6 × 10–3

0.055

HOXD13

cg04415176

3.5 × 10–3

0.057

cg20697025

1.9 × 10–3

0.062

EHD1

cg06154903

1 × 10–4

17.7

ACOT7

cg11699125

1.6 × 10–3

18.1

LOC399815;FAM24B

cg10241347

3.6 × 10–4

19

CDKL2

cg05982271

6.5 × 10–3

19.3

RDH10

cg17662034

2.2 × 10–4

24

  1. The 10 probes with the largest positive and negative fold change (FC) from each patient group, using healthy controls as a reference, are shown.
  2. FC range < 1 indicates less methylation in patients than in controls, while the opposite is true for FC range > 1.
  3. FDR false discovery rate.