Fig. 3

MATCHER accurately infers known correlations between DNA methylation and gene expression. a–c Heatmaps comparing true correlations between gene expression and DNA methylation of related regions (H3K27me3 peaks, LMRs, and P300 binding sites). The first column of each heatmap shows the true correlation based on known correspondence information, the second column shows the correlation inferred by MATCHER in the same dataset, and the third column is correlation inferred by MATCHER using a completely different single cell RNA-seq dataset from mESCs grown in serum. d, e Scatterplot representation of the results shown in (a–c). d Correlations computed using the Angermueller data. e Correlations computed from the Kolodziejczyk data. Each point represents the true and inferred correlation for a single gene-site pair; ideal results would lie along the y = x line. Note that the sign of the inferred correlation is correct for the vast majority of pairs