Fig. 5

Relationship between gene expression and DNA methylation in transition from ground state to primed pluripotency. a Scatterplot showing the relationship between master time inferred from gene expression and master time inferred from DNA methylation. Points are colored by the log10 expression of Rex1. The dotted line is the y = x line. Note that the gene expression and DNA methylation master time values are more correlated before master time = 0.3 than after. b, c Density plots showing the distribution of pseudotime inferred from b gene expression and c DNA methylation. The vertical dotted line indicates the 30th percentile of pseudotime (master time = 0.3). d Violin plot showing the distribution of Rex1 expression in cells before master time = 0.3 (“early”) and after master time = 0.3 (“late”). e Expression of Dnmt3b as a function of gene expression master time. The red line is a LOESS smoothing function indicating the overall expression trend. The black vertical line indicates master time = 0.3. f Expression of Tet1 as a function of gene expression master time. The red line is a LOESS smoothing function indicating the overall expression trend