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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.
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