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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