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Table 2 Results of adjusted linear regression models testing for differential methylation

From: Association between acetaminophen metabolites and CYP2E1 DNA methylation level in neonate cord blood in the Boston Birth Cohort

CpG site

%Difference (95% CI) in DNAm: comparing detected group with not detected group

P-value (robust)

FDR

Genomic coordinate (GRCh37/hg19)

Gene Name

Feature categorya

Relation to CpG Island

cg13315147

− 4.34% (− 7.9%, − 0.8%)

9.84E−04*

0.028

chr10:135341528

CYP2E1

Body

Island

cg05473257

− 4.71% (− 8.6%, − 0.9%)

3.43E−03

0.038

chr10:135341443

CYP2E1

Body

Island

cg23400446

− 4.31% (− 7.9%, − 0.7%)

4.09E−03

0.038

chr10:135342560

CYP2E1

Body

Island

cg05194426

− 5.77% (− 10.6%, − 1%)

9.85E−03

0.045

chr10:135343193

CYP2E1

Body

South Shore

cg19469447

− 3.98% (− 7.2%, − 0.7%)

1.01E−02

0.040

chr10:135341870

CYP2E1

Body

Island

cg10862468

− 3.76% (− 6.9%, − 0.6%)

1.12E−02

0.045

chr10:135342218

CYP2E1

Body

Island

cg25330361

− 3.56% (− 6.2%, − 0.9%)

7.69E−03

0.045

chr10:135342413

CYP2E1

Body

Island

cg03134882

− 3.95% (− 7.3%, − 0.6%)

1.80E−02

0.063

chr10:135341463

CYP2E1

Body

Island

cg19571004

− 1.26% (− 2.5%, 0%)

2.88E−02

0.086

chr10:135340850

CYP2E1

TSS200

North Shore

cg00321709

− 5.75% (− 10.2%, − 1.3%)

3.08E−02

0.086

chr10:135341933

CYP2E1

Body

Island

cg19721068

0.91% (− 0.2%, 2%)

4.60E−02

0.117

chr10:135346592

CYP2E1

Body

Open sea

cg11445109

− 2.98% (− 6%, 0%)

5.31E−02

0.124

chr10:135343248

CYP2E1

Body

South Shore

cg18984983

− 3.21% (− 5.8%, − 0.6%)

9.61E−02

0.207

chr10:135342936

CYP2E1

Body

South Shore

cg24530264

− 3.14% (− 5.6%, − 0.7%)

1.14E−01

0.228

chr10:135342620

CYP2E1

Body

South Shore

cg00436603

0.62% (− 0.6%, 1.8%)

2.98E−01

0.557

chr10:135340740

CYP2E1

TSS200

North Shore

cg26065573

0.44% (− 0.2%, 1%)

3.48E−01

0.609

chr10:135339469

CYP2E1

TSS1500

North Shore

cg09208540

− 0.19% (− 0.6%, 0.3%)

4.07E−01

0.671

chr10:135340467

CYP2E1

TSS1500

North Shore

cg21024264

− 0.55% (− 1.9%, 0.8%)

4.65E−01

0.686

chr10:135341025

CYP2E1

1stExon

North Shore

cg07381788

− 0.15% (− 0.8%, 0.5%)

4.60E−01

0.686

chr10:135340445

CYP2E1

TSS1500

North Shore

cg01355198

− 0.09% (− 0.6%, 0.4%)

5.04E−01

0.706

chr10:135347330

CYP2E1

Body

Open sea

cg05417377

0.18% (− 0.9%, 1.3%)

6.17E−01

0.823

chr10:135350807

CYP2E1

Body

Open sea

cg16538390

− 0.15% (− 0.8%, 0.5%)

6.89E−01

0.838

chr10:135344917

CYP2E1

Body

South Shelf

cg14250048

− 0.02% (− 1%, 1%)

6.86E−01

0.838

chr10:135340785

CYP2E1

TSS200

North Shore

cg01465364

− 0.06% (− 1.3%, 1.1%)

8.47E−01

0.949

chr10:135340721

CYP2E1

TSS200

North Shore

cg10986462

0.46% (− 1.4%, 2.3%)

8.34E−01

0.949

chr10:135340539

CYP2E1

TSS1500

North Shore

cg19837601

0.09% (− 1.3%, 1.5%)

8.91E−01

0.960

chr10:135340871

CYP2E1;CYP2E1

5'UTR;1stExon

North Shore

cg08472147

0.03% (− 1%, 1%)

9.67E−01

0.994

chr10:135340583

CYP2E1

TSS1500

North Shore

cg00720244

0.06% (− 0.4%, 0.5%)

9.94E−01

0.994

chr10:135347434

CYP2E1

Body

Open sea

  1. Results are shown at each of the 28 CpGs located in CYP2E1, between participants with (n = 96) and without (n = 474) acetaminophen detection, sorted by P-value
  2. DNAm DNA methylation, FDR false discovery rate, chr chromosome. Difference in percent DNAm was calculated from adjusted linear regression models with DNAm beta value as the dependent variable. P-value and FDR were obtained from adjusted linear regression models with DNAm M-value as the dependent variables. The P-values are the original P-values before adjustment for multiple testing. CpG sites with P-value < 1.79 × 10−3 (Bonferroni corrected threshold) were marked with asteroid (*). CpG sites with FDR < 0.05 were bolded. Covariates are child sex, delivery type, parity, gestational age, birthweight, maternal age, maternal marital status, prenatal smoking, prenatal alcohol use, intrauterine inflammation, preeclampsia, diabetes mellitus, maternal stress, estimated cell types and 2 surrogate variables. aGene element type obtained from UCSC database: TSS, transcription start site; TSS200, 200 bases from TSS; TSS1500, 1500 bases from TSS; UTR, untranslated region
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Clinical Epigenetics

ISSN: 1868-7083

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