Additional file 1 of The inactive X chromosome accumulates widespread epigenetic variability with age
Creators: name: Liu, Yunfeng
name: Sinke, Lucy
name: Jonkman, Thomas H.
name: Slieker, Roderick C.
name: van Zwet, Erik W.
name: Daxinger, Lucia
name: Heijmans, Bastiaan T.
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Table S1 Characteristics of cohorts used in present study. Table S2 The number and percentage of aDMCs and aVMCs in XCI related annotation features. Fig. S1 Comparison of aDMCs effect size in both sex between DGLM and limma. Fig. S2 Scatter plot of standard error for aDMCs effect size observed in males and females in the discovery data set (BIOS Blood). Fig. S3 UpSet plot showing number of statistically significant overlapping aDMCs in males (a) and females (b) between discovery cohort (BIOS blood) and replication cohort (Johansson Blood and Reynolds Monocytes). Horizontal bars on the lower left corner of figure represent the number of aDMCs detected in the discovery data set and the subsets replicated in the two external data sets. The number of shared aDMCs between data sets represented as vertical bars and the data-sets involved with dots connected with lines. The vertical orange bar represents the number of aDMCs observed in all 3 data sets and are considered replicated aDMCs. Abbreviations: aDMCs age-related differentially methylated CpGs. Fig. S4 Examples of replicated aDMCs and aVMCs in females and males. Left scatter plot showing aDMCs that change in average DNA methylation with age. The aDMCs methylation (mean effects: middle line indicated) increased or decreased with age. Right scatter plot showing aVMCs methylation that change in variance with age. The aVMCs methylation variance (dispersion effect: extra two lines indicated) increased or decreased with age. DNA methylation value were rank-inverse normal transformed (y-axis). Abbreviations: aDMCs age-related differentially methylated CpGs, aVMCs age-related variably methylated CpGs. The CpGs were selected from the top 10 lowest p-values per category. Fig. S5 UpSet plot showing number of statistically significant overlapping aVMCs in males (a) and females (b) between discovery cohort (BIOS blood) and replication cohort (Johansson Blood and Reynolds Monocytes). Horizontal bars on the lower left corner of figure represent the number of aVMCs detected in the discovery data set and the subsets replicated in the two external data sets. The number of shared aVMCs between data sets represented as vertical bars and the data-sets involved with dots connected with lines. The vertical orange bar represents the number of aVMCs observed in all 3 data sets and are considered replicated aVMCs. Abbreviations: aVMCs age-related variably methylated CpGs. Fig. S6 Comparison of replicated aDMCs catalogue in our study with previous study. a Li et al. vs Kananen et al. b Li et al vs Our study. c Kananen et al vs Our study. Fig. S7 Histogram of test statistics for aDMCs in males (a) and females (b) separately. The black line represents the overall fit, the red line is the fit of empirical null distribution with estimated mean and variance. The green and blue lines represent the proportion of true positively and true negatively associations.