Table 3 Top 20 most significant differentially methylated regions (DMRs) associated with Braak stage identified by both coMethDMR and comb-p in meta-analysis.

From: Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer’s disease

     

coMethDMR

 

comb-p

 

Region

GREAT annotation

Illumina annotation

No. probes

Estimate

P-value

FDR

Sidak P-value

Estimate_direction

chr19:49220102–49220485

MAMSTR (+2684); FUT2 (+21062)

MAMSTR

4

0.061

6.02E−16

2.41E−11

1.32E−28

++++

chr7:27153580–27153944

HOXA2 (−11332); HOXA3 (+5452)

HOXA3

6

0.084

1.16E−14

2.32E−10

1.59E−47

++++

chr7:27146237–27146445

HOXA2 (−3911)

HOXA3

4

0.066

2.23E−14

2.37E−10

2.06E−32

++++

chr7:27154262–27155548

HOXA2 (−12475); HOXA3 (+4309)

HOXA3

10

0.047

2.37E−14

2.37E−10

6.19E−27

++++

chr7:27179161–27179432

HOXA4 (−8879); HOXA5 (+3990)

NA

3

0.045

1.35E−12

1.08E−08

2.60E−21

++++

chr5:27038605–27038836

CDH9 (−28)

CDH9

3

0.059

2.14E−12

1.22E−08

1.00E−11

++++

chr7:27140797–27141139

HOXA1 (−5375); HOXA2 (+1462)

HOXA2

5

0.048

3.44E−12

1.72E−08

2.79E−19

++++

chr19:10736006–10736448

SLC44A2 (+293)

SLC44A2

7

0.058

7.79E−12

3.11E−08

2.13E−38

++++

chr1:7692321–7692367

VAMP3 (−138,985); CAMTA1 (+846,960)

CAMTA1

3

−0.052

9.58E−12

3.19E−08

2.13E−12

– – – –

chr17:46685292–46685448

HOXB6 (−3016)

HOXB7

3

0.046

1.49E−11

4.59E−08

2.58E−09

++++

chr17:46698881–46699155

HOXB8 (−6717); HOXB9 (+4821)

HOXB9

4

0.038

1.95E−11

5.56E−08

2.40E−20

++++

chr6:138866865–138867125

ECT2L (−250068); HEBP2 (+141639)

NHSL1

7

0.025

4.12E−11

1.10E−07

1.82E−22

++++

chr6:10556147–10556523

GNT6 (−77658); GCNT2 (+27746)

GCNT2

3

0.070

7.84E−11

1.96E−07

4.69E−20

++++

chr7:27143046–27143806

HOXA2 (−996)

HOXA2

11

0.042

1.04E−10

2.45E−07

6.42E−21

++++

chr7:98739496–98739782

SMURF1 (+2084); TRRAP (+263526)

SMURF1

4

0.044

1.22E−10

2.71E−07

4.04E−11

++++

chr19:827715–827843

AZU1 (−47)

AZU1

3

−0.033

2.10E−10

4.20E−07

5.87E−16

– – – –

chr19:6476756–6477198

DENND1C (+4842); CRB3 (+12683)

DENND1C

3

0.034

3.78E−10

6.86E−07

3.60E−13

++++

chr11:72533295–72533664

ATG16L2 (+8127); FCHSD2 (+319826)

ATG16L2

3

0.064

8.07E−10

1.29E−06

1.20E−20

++++

chr20:57582581-57583709

CTSZ (−843)

CTSZ

16

−0.037

8.03E−10

1.29E−06

2.49E−18

– – – –

chr5:172175604-172175855

DUSP1 (+22468); NEURL1B (+107461)

NA

4

0.027

1.07E−09

1.62E−06

2.22E−11

++++

  1. For each DMR, annotations include location of the DMR based on hg19/GRCh37 genomic annotation (Region), nearby genes based on GREAT, and Illumina gene annotations. The inverse-variance weighted meta-analysis regression models results based on coMethDMR include the number of probes in the DMR (No. Probes), estimated effect size (Estimate) where DMRs that are hypermethylated in AD have positive values, P-value, and false discovery rate (FDR) for multiple comparison corrections. Meta-analysis results based on comb-p include multiple comparison corrected P-value based on Sidak method (Sidak P-value). The last column (Estimate_Direction) indicates the direction of DMR effects estimated by coMethDMR in Gasparoni, London, Mount Sinai, and ROSMAP cohorts where + indicates hypermethylation in AD and − indicates hypo-methylation in AD in an individual cohort. All P-values are two-sided.
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