TABLE 7.
Weighted gene co-methylation network analysis (WGCNA) modules (n = 11) significantly associated with the initiation of HAART in PLWH.
| Co-methylation modulea | # of CpGs in module | Module eigenvector methylationc | # (%) of CpGs with kME 0.85 | |||
|---|---|---|---|---|---|---|
| Visit 1 mean (SD) | Visit 2 mean (SD) | Eigenvector changed | p-valuee | |||
| 1 | 133,037 | −0.017 (0.027) | −0.004 (0.024) | ↑ 0.013 | 3.3 × 10−6 | 37,284 (28) |
| 4 | 9,775 | −0.018 (0.021) | −0.006 (0.024) | ↑ 0.012 | 3.5 × 10−7 | 1,596 (16) |
| 5 | 5,615 | 0.022 (0.020) | 0.013 (0.021) | ↓ 0.009 | 1.8 × 10−5 | 672 (12) |
| 6 | 5,184 | −0.012 (0.024) | −0.003 (0.025) | ↑ 0.009 | 6.8 × 10−5 | 892 (17) |
| 8 | 1,677 | −0.020 (0.019) | −0.011 (0.023) | ↑ 0.009 | 1.6 × 10−5 | 141 (8) |
| 9 | 1,019 | −0.018 (0.025) | −0.003 (0.024) | ↑ 0.015 | 2.6 × 10−9 | 50 (5) |
| 14 b | 106 | 0.021 (0.026) | 0.011 (0.023) | ↓ 0.010 | 4.9 × 10−4 | 5 (4.7) |
| 15 | 94 | 0.015 (0.025) | 0.003 (0.024) | ↓ 0.012 | 2.6 × 10−6 | 1 (1) |
| 18 b | 38 | −0.025 (0.035) | −0.007 (0.022) | ↑ 0.018 | 4.1 × 10−8 | 17 (45) |
| 19 | 91 | −0.012 (0.023) | −0.003 (0.023) | ↑ 0.009 | 2.3 × 10−4 | 22 (24) |
| 20 | 71 | −0.008 (0.024) | 0.001 (0.025) | ↑ 0.009 | 6.2 × 10−4 | 2 (3) |
a: Each co-methylation module (module numbers shown in bold) is a cluster of CpG methylation sites (CpGs) within the >850,000 sites evaluated on the Infinium MethylationEPIC BeadChip, identified by WGCNA, to be correlated with each other; any one CpG site belongs to only one module. Out of a total of 67 modules identified by WGCNA, identical to the modules reported by Breen et al. (2022), the 11 modules shown are those that are significantly associated with HAART initiation between visit 1 and visit 2 in the PLWH. Modules up to #18 are numbered as assigned by Breen et al. (2022). Modules #19 and 20 are numbered according to the number of CpGs (largest to smallest) contained in those two modules.
b: Modules containing CpGs that fall within pathways with significant adjusted p-values in the enrichment analysis.
c: Methylation levels defined as ratio of intensities, and module eigenvector defined as the first principal component in the module methylation matrix. Data are based on 200 PLWH with observations at both visits 1 and 2.
d: Direction (up arrow = positive or increased methylation; down arrow = negative or decreased methylation) and magnitude of change in the mean module methylation (visit 2 mean module eigenvector–visit 1 module eigenvector).
e: Results from a non-parametric group comparison test (Kruskal–Wallis) comparing the mean module eigenvector methylation from visits 1 to 2 over the course of HAART initiation (PLWH only); the level of significance adjusting for multiple comparisons was p < 0.05/67 or <7.5 × 10−4. No significant differences were observed in the mean module eigen methylation from visits 1 to 2 for any module in SN controls.