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Table 3 Results from sex-by-Braak stage interaction analysis. For each CpG, annotations include the location of the CpG based on hg19/GRCh37 genomic annotation (chr, position), Illumina gene annotations, nearby genes based on GREAT, and chromatin state. The inverse-variance weighted meta-analysis regression model results include estimated effect size (estimate) where CpGs that are hyper-methylated in samples with AD neuropathology have positive values, its associated standard error (se), and P-value. Adj.pval is adjusted P-value from stageR analysis. Shown in bold are significant results (adj.pval < 0.05 for interaction and P-value < 0.05 for one sex). * indicates these CpGs also reached 5% FDR significance in sex-stratified analysis

From: Sex-specific DNA methylation differences in Alzheimer’s disease pathology

cpg

Annotations

Female samples

Male samples

Sex * Braak stage interaction

chr

Position

Illumina

GREAT (distance to TSS)

chromatin state

estimate

se

P-value

estimate

se

P-value

estimate

se

P-value

adj.pval

cg13212831

chr1

56046343

 

USP24(-365558); PPAP2B(+ 998897)

Weak transcription

0.083

0.030

6.15E-03

− 0.139

0.034

4.10E-05

− 0.222

0.044

6.38E-07

3.54E-04

cg25734825

chr3

119182523

TMEM39A

TMEM39A(+ 5)

Active TSS

0.059

0.030

5.01E-02

− 0.156

0.036

1.21E-05

− 0.220

0.045

1.12E-06

6.22E-04

*cg02331272

chr11

66964208

KDM2A;KDM2A

ADRBK1(-69672); KDM2A(+ 77051)

Weak transcription

0.058

0.030

1.10E-01

− 0.166

0.036

2.99E-06

− 0.215

0.046

2.25E-06

1.25E-03

cg10622825

chr1

172413349

PIGC;PIGC;C1orf105

PIGC(-124)

Active TSS

− 0.069

0.030

2.22E-02

0.134

0.034

7.78E-05

0.200

0.045

7.00E-06

3.88E-03

cg10784067

chr16

14014435

ERCC4

ERCC4(+ 422)

Active TSS

− 0.127

0.032

5.33E-05

0.068

0.033

3.78E-02

0.201

0.045

9.03E-06

5.01E-03

cg14284055

chr1

24439399

MYOM3

MYOM3(-735)

Bivalent Enhancer

0.115

0.029

8.28E-05

− 0.066

0.037

7.12E-02

− 0.193

0.045

1.94E-05

1.07E-02

*cg18942110

chr15

91072797

CRTC3;CRTC3

CRTC3(-502)

Active TSS

0.031

0.030

3.06E-01

− 0.164

0.035

2.23E-06

− 0.187

0.045

3.13E-05

1.74E-02

cg09342330

chr14

89021109

PTPN21;PTPN21

PTPN21(-33)

Active TSS

0.045

0.030

1.31E-01

− 0.144

0.037

8.30E-05

− 0.189

0.046

3.47E-05

1.93E-02

cg21722170

chr6

31977443

TNXB;TNXA

C4B(-5095); C4A(+ 27643)

Quiescent/Low

0.034

0.030

2.53E-01

− 0.148

0.034

1.57E-05

− 0.183

0.045

4.17E-05

2.31E-02

cg03662217

chr21

35747882

FAM165B

SMIM11(-20)

Active TSS

0.039

0.029

1.85E-01

− 0.141

0.036

7.27E-05

− 0.184

0.045

4.59E-05

2.55E-02

cg15026265

chr12

28283812

 

PTHLH(-158910); CCDC91(-59566)

Quiescent/Low

− 0.038

0.029

1.95E-01

0.134

0.033

6.58E-05

0.176

0.044

6.72E-05

3.73E-02

cg00659421

chr7

86781760

DMTF1;DMTF1;DMTF1;DMTF1;DMTF1;DMTF1;DMTF1

DMTF1(-109)

Active TSS

− 0.050

0.031

1.08E-01

0.130

0.033

7.53E-05

0.178

0.045

6.95E-05

3.86E-02

*cg24917065

chr8

23418389

SLC25A37

SLC25A37(+ 32072); NKX3-1(+ 122050)

Quiescent/Low

− 0.135

0.030

6.26E-06

0.042

0.033

2.05E-01

0.174

0.044

6.98E-05

3.87E-02

*cg18281939

chr5

77783895

LHFPL2

SCAMP1(+ 127557); LHFPL2(+ 160752)

Weak transcription

− 0.022

0.029

4.55E-01

− 0.179

0.036

6.26E-07

− 0.177

0.045

7.10E-05

3.94E-02