Table 1.
PCA loading matrix‡ | ||||||
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CpG no. | Illumina ID | DNAm-β | UCSC RefGene Group* | Modified position category† | PC1, 16.2% | PC2, 13.3% |
1 | cg12944573 | 0.56 | TSS | Promoter | 0.42§ | 0.52§ |
2 | cg17256711 | 0.24 | TSS | Promoter | 0.32§ | 0.23 |
3 | cg13245264 | 0.68 | 1st Exon (Exon 11) | Promoter | 0.12 | 0.44§ |
4 | cg10143581 | 0.88 | TSS | Promoter | 0.04 | 0.36§ |
5 | cg22370006 | 0.15 | TSS | Promoter | 0.44§ | −0.09 |
6 | cg14262937 | 0.16 | TSS | Promoter | 0.41§ | −0.11 |
7 | cg06649410 | 0.19 | 1st Exon (Exon 1) | Promoter | — | — |
8 | cg05215925 | 0.13 | 1st Exon (Exon 1) | Promoter | 0.74§ | −0.22 |
9 | cg12838303 | 0.13 | 1st Exon (Exon 1) | Promoter | 0.74§ | −0.21 |
10 | cg22719623 | 0.44 | 1st Exon (Exon 1) | Promoter | 0.70§ | 0.02 |
11 | cg15085086 | 0.21 | 1st Exon (Exon 1) | Promoter | 0.38§ | −0.47 |
12 | cg05017309 | 0.88 | Body | Body | 0.00 | 0.12 |
13 | cg22366819 | 0.91 | Body | Body | 0.37§ | 0.50§ |
14 | cg12466324 | 0.79 | Body | Body | −0.61 | 0.45§ |
15 | cg23384428 | 0.93 | Body | Body | 0.16 | 0.58§ |
16 | cg11881038 | 0.78 | Body | Body | — | — |
17 | cg04170440 | 0.85 | Body | Body | 0.20 | 0.59§ |
18 | cg07813322 | 0.85 | 3’UTR | Body | −0.31 | 0.13 |
19 | cg15658985 | 0.86 | Body | Body | −0.08 | −0.52 |
20 | cg26415516 | 0.78 | 3’UTR | Body | −0.27 | 0.08 |
21 | cg27296341 | 0.68 | Body | Body | 0.44§ | 0.09 |
22 | cg10276116 | 0.92 | Body | Body | −0.01 | 0.47§ |
23 | cg07356123 | 0.87 | Body | Body | 0.21 | 0.38§ |
DNAm-β = DNA methylation β; OPRM1 = opioid receptor mu-1 gene; PC = principal component; PCA = principal component analysis; TSS = transcription start site; UTR = untranslated region; UCSC = University of California, Santa Cruz.
Annotations according to the UCSC database (http://genome.ucsc.edu/)
Modified position categorizations, as adopted from Sandoval and colleagues.41
Percentages represent the proportion of variance among CpG DNA methylation explained by the principal component.
Positive PC loading ≥ 0.30, as suggested previously for data with sample sizes ≥ 100.45