Table 5. Strain-dependent differentially methylated CpGs/regions detected by both Illumina human MethylationEPIC probes and by MBD-seq.
| EPIC1 | MBD-seq1 | ||||||
|---|---|---|---|---|---|---|---|
| ProbeID | Gene3 | Region4 | Position (mm10) 3 | Coef.2 | Strain (P) | logFC2 | Strain (P) |
| Differentially methylated CpGs detected by EPIC probe at FDR 10%; replicated by MBD-seq | |||||||
| cg21064315 | SZT2 | 3'UTR; Shore | chr4:118.36 | -0.82 | 5.5E-09 | -2.0 | 1.7E-04 |
| cg14945867 | CNIH | 1stExon; Island | chr14:46.79 | 0.27 | 1.3E-06 | 6.0 | 1.2E-09 |
| cg04546815 | KANK4 | Body | chr4:98.78 | 0.34 | 1.6E-06 | 1.7 | 4.4E-04 |
| cg10277781 | CNIH | 1stExon; Island | chr14:46.79 | 0.35 | 1.9E-06 | 6.0 | 1.2E-09 |
| cg00049718 | CSDE1 | 5'UTR | chr3:103.02 | 0.40 | 2.6E-06 | 6.8 | 9.8E-15 |
| cg07211292 | C20orf160 | 3'UTR; Island | chr2:153.08 | -0.46 | 5.0E-06 | -1.5 | 1.4E-05 |
| cg24255125 | GRIK4 | Body; Island | chr9:42.52 | -0.36 | 7.8E-06 | -3.0 | 5.9E-09 |
| cg03517030 | MTCH2 | 1stExon; Island | chr2:90.85 | 0.35 | 1.6E-05 | 6.7 | 2.3E-14 |
| cg05781968 | WNT5A | Body; Island | chr14:28.51 | 0.31 | 4.4E-05 | 2.3 | 1.0E-05 |
| cg04154281 | UBTF | Body; Shore | chr11:102.31 | 0.17 | 6.5E-05 | 0.7 | 0.03 |
| cg06861375 | ZNF697 | Body; Island | chr3:98.43 | 0.36 | 6.7E-05 | 4.5 | 2.8E-04 |
| cg24959134 | - | - | chr10:92.44 | -0.33 | 9.4E-05 | -2.4 | 0.01 |
| cg06552810 | - | - | chr2:106.19 | 0.26 | 1.1E-04 | 2.9 | 0.002 |
| cg01663821 | Shore | chr3:98.94 | 0.19 | 1.3E-04 | 0.9 | 0.02 | |
| cg00597112 | - | - | chr11:109.01 | 0.21 | 1.4E-04 | 0.5 | 0.002 |
| cg26857408 | UBTF | Body; Shore | chr11:102.31 | 0.24 | 2.1E-04 | 0.7 | 0.03 |
| cg15172734 | SLMAP | 5'UTR; Shore | chr14:26.53 | -0.11 | 3.4E-04 | -2.5 | 0.01 |
| cg09990537 | WNT5A | 5'UTR; Shore | chr14:28.51 | 0.17 | 3.4E-04 | 1.0 | 0.004 |
| cg12849734 | - | - | chr2:157.71 | 0.14 | 4.4E-04 | 0.9 | 0.01 |
| cg21746387 | NDUFA4L2 | TSS1500; Shore | chr10:127.51 | -0.17 | 5.5E-04 | -3.4 | 0.001 |
| cg11382417 | - | - | chr2:96.32 | -0.21 | 6.0E-04 | -4.7 | 1.3E-07 |
| cg02865068 | - | Shore | chr2:105.66 | 0.11 | 9.7E-04 | 2.9 | 0.04 |
| cg14275842 | CHRNE | Body; Island | chr11:70.62 | 0.18 | 0.001 | 1.0 | 0.005 |
| cg02159996 | GABRR1 | 5'UTR | chr4:33.13 | 0.13 | 0.001 | 1.2 | 2.5E-04 |
| cg00920372 | - | - | chr19:45.33 | -0.08 | 0.001 | -1.5 | 8.8E-04 |
| cg03422015 | ERC1 | Body | chr6:119.69 | 0.04 | 0.001 | 1.1 | 0.02 |
| cg04340318 | - | - | chr4:86.04 | 0.16 | 0.001 | 2.3 | 0.001 |
| cg14465355 | DYNC1H1 | Body; Shore | chr12:110.64 | 0.06 | 0.001 | 0.6 | 0.02 |
| cg15002641 | SOX13 | Body | chr1:133.39 | -0.10 | 0.001 | -1.0 | 0.02 |
| Differentially methylated regions detected by MBD-seq at FDR 10%; replicated by EPIC | |||||||
| cg05362127 | WNT5A | TSS200; Island | chr14:28.51 | 0.33 | 0.002 | 2.3 | 9.4E-06 |
| cg24142850 | - | - | chr8:92.55 | -0.09 | 0.005 | -2.9 | 9.4E-05 |
| cg15585318 | WNT5A | Body; Island | chr14:28.51 | 0.22 | 0.006 | 1.8 | 2.1E-06 |
| cg09595163 | WNT5A | Body; Island | chr14:28.51 | 0.18 | 0.006 | 2.3 | 1.2E-05 |
| cg13868216 | BAIAP2L2 | Body; Island | chr15:79.26 | 0.11 | 0.01 | 1.6 | 1.8E-04 |
| cg09972454 | PDXDC1 | Body; Shore | chr4:147.94 | -0.06 | 0.01 | -2.9 | 1.5E-06 |
| cg18120446 | - | Island | chr5:41.75 | 0.01 | 0.02 | -2.2 | 2.7E-08 |
1These are strain-dependent differentially methylated CpGs (EPIC microarray) and CpG regions (MBD-seq) based on a “false discovery threshold” (FDR) cutoff of 10% and replication at an uncorrected p-value threshold of 0.05.
2Coef. is the linear regression coefficient (i.e., difference in methylation relative to C57BL/6J; negative is lower methylation in DBA/2J; and positive is higher methylation in DBA/2J compared to C57BL/6J). LogFC is log2 fold difference in methylation (i.e., difference in methylation relative to DBA/2J; negative is lower methylation in DBA/2J; and positive is higher methylation in DBA/2J compared to C57BL/6J).
3CpG location in relation to gene features and CpG region based in probe annotations for the human methylation microarray. For most conserved regions, mouse annotations are analogous to humans.
4Chromosome and Megabase coordinate based on mm10 mouse reference genome