Table 2. The ten top-ranked cross-cortex Braak-associated DMPs.
Shown for each DMP are chromosomal location (hg19), up/downstream genes, Fisher’s P-value, Brown’s P-value, and cross-cortex estimate (Δ) of methylation difference between individuals with the lowest (score 0) and highest (score VI) Braak stage. Also shown are differences (Δ) between Braak 0 and Braak IV and corresponding P values from our individual cortex models in the London discovery cohort (see Online Methods) and the STG and PFC in the Mount Sinai replication cohort for CpG sites showing a nominally significant difference in the same direction. The 100 top-ranked cross-cortex Braak-associated DMPs are given in Supplementary Table S9.
| Probe Information | London Cohort | Mount Sinai Cohort | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cross-cortex model | EC | STG | PFC | CER | STG | PFC | |||||||||||||
| Probe | Position | Illumina Annotation | Genes with TSS within 5Kb upstream |
Genes with TSS within 1Kb downstream |
Fisher’s P Value |
Brown’s P Value |
Δ | P value | Δ | P value | Δ |
P value |
Δ | P value | Δ | P value | Δ | P value | Δ |
| cg11823178 | 8:41519399 | ANK1;MIR486 | NKX6-3 | ANK1 | 3.42E–11 | 1.00E–06 | 3.20 | 4.59E–07 | 4.62 | 6.51E–05 | 3.12 | 2.33E–03 | 2.05 | - | - | 1.63E–04 | 3.36 | 1.07E–03 | 2.97 |
| cg25018458 | 17:980014 | ABR | TIMM22 | ABR | 1.89E–10 | 9.91E–07 | 1.34 | 1.05E–04 | 1.29 | 4.36E–06 | 1.59 | 9.48E–04 | 1.12 | - | - | 4.46E–05 | 1.82 | 2.14E–04 | 1.93 |
| cg05810363 | 17:74475270 | RHBDF2 | RHBDF2 | AANAT | 9.42E–10 | 9.15E–06 | 3.36 | 1.37E–04 | 3.79 | 2.26E–05 | 3.58 | 7.93E–04 | 2.76 | - | - | 3.55E–03 | 3.65 | 5.54E–03 | 3.19 |
| cg05066959 | 8:41519308 | ANK1;MIR486 | NKX6-3 | ANK1 | 1.24E–09 | 6.24E–06 | 4.26 | 1.35E–05 | 5.45 | 3.78E–04 | 4.03 | 6.48E–04 | 3.45 | - | - | 5.78E–04 | 4.75 | 4.00E–03 | 3.41 |
| cg18428542 | 2:91787196 | - | ACTR3BP2 | - | 1.94E–09 | 2.53E–05 | −4.00 | 2.09E–04 | −4.05 | 1.73E–04 | −3.93 | 1.47E–04 | −4.04 | 7.46E–05 | −4.43 | - | - | - | - |
| cg16665310 | 13:100218136 | - | CLYBL | TM9SF2 | 6.11E–09 | 1.11E–04 | −5.73 | 1.39E–04 | −6.71 | 1.17E–04 | −5.15 | 1.13E–03 | −5.50 | 2.32E–04 | −3.84 | - | - | - | - |
| cg05912299 | 13:100217962 | - | CLYBL | TM9SF2 | 7.17E–09 | 1.38E–04 | −6.03 | 6.76E–05 | −7.46 | 3.67E–03 | −4.64 | 8.85E–05 | −6.29 | 9.86E–04 | −5.63 | - | - | - | - |
| cg03169557 | 16:89598950 | SPG7 | RPL13 | SPG7 | 7.95E–09 | 7.91E–06 | 1.63 | 3.01E–04 | 1.31 | 1.35E–04 | 1.97 | 6.05E–04 | 1.52 | - | - | 2.85E–03 | 2.11 | 7.98E–04 | 2.34 |
| cg23968456 | 10:73521631 | CDH23;C10orf54 | C10orf105 | C10orf54 | 1.09E–08 | 1.09E–05 | 1.22 | 1.89E–03 | 0.87 | 2.21E–03 | 1.13 | 8.27E–06 | 1.62 | - | - | 3.07E–03 | 1.72 | 0.0416 | 1.05 |
| cg02672452 | 2:91818189 | - | ACTR3BP2 | - | 1.16E–08 | 1.27E–04 | −4.42 | 4.71E–05 | −5.29 | 2.35E–03 | −3.64 | 3.33E–04 | −4.49 | 6.75E–04 | −5.87 | - | - | - | - |