Fig. 6
Data visualization and exploration on the Cellular Lifespan ShinyApp. (A–C) Visualization example of high-dimensionality epigenetic DNA methylation (DNAm) data using tools on the ShinyApp. (A) Interactive timecourse of the DNAm Skin&Blood clock (Horvath2, a multivariate algorithm trained using penalized elastic net regression) across the cellular lifespan of HC1 fibroblasts, both untreated (grey) and treated chronically (red) with 100 nM of dexamethasone (DEX, glucocorticoid receptor agonist) to mimic chronic stress exposure. Note that the x axis represents time in culture, which can be changed using the selector menu on the left to “population doublings” to take into account the reduced division rate in Dex-treated cells. Other biological measures are visualized via tabs on the top. (B,C) Interactive principal component analysis of the 45,000 significant age-related CpGs in 2D (B) and 3D (C). The frequency and duration of different cytological, molecular, and bioenergetic measurements vary by cell lines and experimental conditions. See Figs. 3,4, Tables 2,3, and Supplemental Fig. 1 for details. The Shiny App can be accessed, and the data downloaded, at https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study.
