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Table 2 Age-associated methylation predicted to mediate the relationship between age and expression of oxidative phosphorylation, ribosome, and autophagy genes

From: Transcriptomic profiles of aging in purified human immune cells

Age ~ Methylation

Methylation ~ cis Gene expression

Age ~ Gene expression

CpG ID

Chr

Cor

FDR

Gene

Cor

FDR

Indirect

Direct

Total

Beta (SE)

P-value

Beta (SE)

P-value

Beta (SE)

FDR

Oxidative phosphorylation genes from gene ontology (GO:0006119):

cg07388493

1

−0.4

2.4E-42

NDUFS5

0.22

1.1E-12

−0.097 (0.014)

2.7E-12

−0.09 (0.03)

1.9E-03

−0.19 (0.03)

1.2E-08

cg24704287

19

−0.17

1.6E-07

NDUFB7

0.16

1.3E-05

−0.037 (0.009)

1.8E-05

−0.11 (0.03)

1.8E-05

−0.15 (0.03)

9.4E-06

cg09267188

8

−0.14

2.1E-05

UQCRB

−0.13

1.1E-03

0.028 (0.007)

3.7E-05

0.10 (0.03)

9.3E-05

0.13 (0.03)

1.0E-05

cg27246938

7

−0.11

7.5E-04

NDUFB2

−0.24

2.5E-14

0.030 (0.007)

6.1E-05

−0.14 (0.03)

1.1E-07

−0.11 (0.03)

1.2E-04

cg09876992

22

−0.32

3.3E-26

NDUFA6

−0.13

8.5E-04

−0.027 (0.007)

1.8E-04

−0.17 (0.03)

7.2E-10

−0.20 (0.03)

6.9E-04

Ribosome genes from gene ontology (GO:005840):

cg17328880

19

−0.25

3.4E-16

MRPL34

0.29

4.0E-22

−0.070 (0.01)

7.6E-12

−0.07 (0.03)

4.8E-03

−0.14 (0.03)

3.0E-06

cg04865726

1

−0.27

7.5E-19

MRPL20

0.24

1.2E-14

−0.069 (0.011)

7.7E-11

−0.12 (0.03)

3.9E-06

−0.19 (0.03)

9.2E-09

cg08885076

2

−0.2

8.1E-11

MRPL30

0.2

7.6E-10

−0.042 (0.008)

6.9E-08

−0.05 (0.03)

5.3E-02

−0.09 (0.03)

1.1E-03

cg16399745

12

−0.29

6.4E-21

MRPL51

−0.15

8.4E-05

0.036 (0.008)

5.5E-06

−0.15 (0.03)

1.1E-08

−0.12 (0.03)

6.6E-05

cg16604233

6

−0.26

3.0E-17

RPS18

−0.16

4.6E-06

0.042 (0.01)

1.6E-05

−0.16 (0.03)

8.1E-08

−0.11 (0.03)

1.3E-04

cg16000022

11

−0.16

1.8E-06

MRPL21

−0.15

4.9E-05

0.028 (0.007)

2.8E-05

0.10 (0.03)

1.3E-04

0.13 (0.03)

6.9E-06

cg17614703

5

0.14

3.2E-05

CANX

−0.13

7.7E-04

0.028 (0.007)

2.9E-05

0.10 (0.03)

8.2E-05

0.13 (0.03)

3.2E-05

cg15829665

6

−0.12

5.5E-04

MRPL18

−0.13

1.3E-03

0.028 (0.007)

3.6E-05

0.10 (0.03)

9.3E-05

0.13 (0.03)

4.6E-05

cg21252105

9

−0.18

2.8E-08

MRPL41

0.15

4.3E-05

−0.035 (0.009)

7.8E-05

−0.10 (0.03)

2.2E-04

−0.13 (0.03)

2.7E-05

cg14663914

19

−0.11

1.1E-03

RPS15

0.17

1.7E-06

−0.027 (0.007)

8.9E-05

−0.17 (0.03)

1.5E-09

−0.20 (0.03)

6.5E-06

cg05017994

5

0.16

9.4E-07

MRPL36

−0.15

2.3E-05

−0.039 (0.01)

9.6E-05

−0.14 (0.03)

3.2E-07

−0.18 (0.03)

1.9E-07

cg23163653

6

−0.16

3.8E-07

ABCF1

−0.13

6.2E-04

−0.027 (0.007)

1.0E-04

−0.17 (0.03)

1.2E-09

−0.20 (0.03)

1.3E-03

cg10700019

8

−0.11

9.8E-04

RPL8

−0.28

5.2E-21

0.033 (0.008)

1.1E-04

0.12 (0.03)

7.7E-06

0.15 (0.03)

1.0E-05

cg27209993

6

−0.14

2.7E-05

MRPS10

0.17

4.0E-07

−0.023 (0.006)

1.3E-04

−0.06 (0.03)

2.7E-02

−0.09 (0.03)

1.1E-03

cg00435173

17

−0.2

3.7E-10

RPL27

0.13

1.1E-03

0.033 (0.009)

1.4E-04

0.12 (0.03)

4.8E-06

0.15 (0.03)

8.0E-04

cg00530414

16

−0.21

8.3E-12

RPS15A

−0.15

3.9E-05

0.030 (0.008)

1.8E-04

−0.13 (0.03)

5.0E-06

−0.09 (0.03)

1.0E-03

cg22803868

17

−0.12

6.1E-04

NUFIP2

−0.14

2.0E-04

0.023 (0.007)

4.7E-04

0.11 (0.03)

8.8E-05

0.13 (0.03)

7.1E-05

cg13084677

4

0.12

3.8E-04

RPL9

0.19

3.5E-09

0.017 (0.006)

4.6E-03

−0.12 (0.03)

1.8E-05

−0.10 (0.03)

7.7E-04

Autophagy genes from Figure 3 :

cg24213719

18

0.19

1.9E-09

BCL2

0.13

7.2E-04

0.028 (0.007)

3.3E-05

0.10 (0.03)

1.4E-04

0.13 (0.03)

1.2E-03

cg11789534

22

−0.17

1.3E-07

IL2RB

0.16

4.1E-06

−0.032 (0.008)

4.6E-05

0.09 (0.02)

4.2E-05

0.06 (0.02)

9.9E-04

cg21826784

1

−0.12

3.4E-04

FRAP1

−0.13

9.5E-04

−0.027 (0.007)

1.2E-04

−0.17 (0.03)

2.2E-09

−0.20 (0.03)

2.3E-05

cg22117188

3

−0.13

1.4E-04

PRKCD

−0.18

1.9E-07

−0.027 (0.007)

1.5E-04

−0.17 (0.03)

5.2E-10

−0.20 (0.03)

8.6E-05

cg18728264

11

−0.19

1.9E-09

IL10RA

0.14

3.9E-04

−0.020 (0.006)

4.3E-04

0.21 (0.03)

1.7E-13

0.19 (0.03)

1.5E-08

  1. CpGs whose degree of methylation significantly associated with age (FDR ≤ 0.001), cis-gene expression (±1 MB; FDR ≤ 0.001), and was predicted to mediate (indirect p-value < 0.05) the total effect (total beta, SE, FDR) of age on gene expression. Results include only the most significant mediating CpG identified per gene for oxidative phosphorylation genes (from Gene Ontology pathway GO:0006119), ribosome genes (from GO:005840) and autophagy genes (from Figure 3), and are sorted first by pathway, then by the significance of the mediation effect (full mediation results are presented in Additional file 2: Table S10). The direct effects of age on gene expression not supported to be mediated by methylation are also shown (direct beta, SE, p-value). Analyses included 1,264 CD14+ monocyte samples; partial correlations (cor) were adjusted for sex, race, study site, residual contamination with non-targeted cells, and microarray chip effects.