Fig 1.
Age effects versus HIV-1 effects on methylation status.
Methylation differences for each of the 24 pairs of samples were calculated and a paired t-test was performed for each of the CpG sites on the 450K array. The HIV-1 effect (X-axis) was measured as the signed logarithm of the Student t-test p-value. Age effects (Y-axis) were measured by the Pearson correlation coefficient with age. Each dot is colored according to its module membership (See Fig. 2). This is a representative figure for both data sets.
Fig 2.
Relating modules to HIV-status and age.
Co-methylation modules for HIV-1 status and aging (A) were identified using the blockwise modules function in WCGNA R package. The significant p values for the modules are indicated as follows: * = p≤0.05, ** = p≤0.01, *** = p≤0.001 (B) A box plot depicting module 3 versus age and HIV status.
Table 1.
Module preservation between data sets.
Table 2.
Estimating accelerated aging due to HIV-1 infection using a multivariate model.
Fig 3.
Heat map of module-trait relationships.
This heat map shows correlations between HIV status, chronological age, and the co-methylation module (represented by their eigenvectors) for data set one (A) and data set two (B). Included are cell subsets whose absolute numbers have an absolute correlation with module 3 that was ≥0.4. Red depicts a positive correlation, blue depicts a negative correlation, as indicated by the color band on the right.
Table 3.
T-cell subsets that correlate with module 3 with a correlation coefficient ≥ 0.34.
Table 4.
Polycomb group target genes (PCGT) represented in module eigenvector 3.