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Table 7 Correlation of differential methylation with differences in transcript levels

From: A combined epigenome- and transcriptome-wide association study of the oral masticatory mucosa assigns CYP1B1 a central role for epithelial health in smokers

Gene

p value (DE)

q value (DE)

log2FC

Best CpG

Chr

Position in bp (hg19a)

Add. CpGs

p value (DM)b

q value (DM)

Δβ/10 SPY

CYP1B1

2.2 × 10−14

1.3 × 10−10

2.94

cg01584760

2

38,296,474

6

3.8 × 10−10

3.1 × 10−4

− 0.046

SLC7A5

1.1 × 10−4

6.5 × 10−2

0.62

cg10099957

16

87,869,757

2

9.6 × 10−6

7.1 × 10−2

− 0.060

LAMA3 c

0.025

0.64

− 0.20

cg16113793

18

21,451,607

1

1.5 × 10−6

4.0 × 10−2

− 0.027

EDC3

0.031

0.65

0.39

cg17181940

15

74,948,075

1

5.6 × 10−6

5.9 × 10−2

− 0.054

  1. Genes nominally significant in the differential expression (DE) analysis that correspond to those CpGs that were associated with smoke pack years (SPY) with q < 0.15 in the differential methylation (DM) analysis and that lie within genetic regions previously reported to be differentially methylated in buccals [22]. EDC3 was additionally reported to be differentially methylated in blood [32]
  2. aNCBI build GRCh37
  3. bp values are from the analysis of covariance (ANCOVA) with adjustment by age, sex and batch. DE differential expression, Log2FC log2fold change, Chr chromosome, bp basepairs, Add. CpGs additional CpGs significant with q < 0.15 at this locus, DM differential methylation, SPY smoke pack years
  4. cEffect sizes for DE and DM are contradictory