Fig. 2: Analysis of DNA methylation and gene expression in E11 embryo.
From: Spatial joint profiling of DNA methylome and transcriptome in tissues
a, Heat map of DNA methylation levels for the top ten differentially methylated genomic loci in brain and spinal cord (cluster W2) of E11 embryo. Each row represents a specific genomic locus and each column represents a different cluster. The colour scale indicates the z scores of DNA-methylation levels. b, Heat map of expression levels for nearby genes corresponding to the genomic loci in a. Each row represents a specific gene and each column represents a different cluster. The colour scale indicates the z scores of gene-expression levels. c, UMAP visualization and spatial mapping of DNA methylation (methylation percentage) and RNA-expression levels (log-normalized expression) for selected marker genes across different clusters. U1, UMAP 1; U2, UMAP2. d, Correlation analysis between DNA methylation and RNA expression of nearby genes. Negative correlations (blue) indicate a repressive effect of methylation, whereas positive correlations (orange) indicate activation. Correlation coefficient and P value were calculated using the two-sided Pearson correlation test and P values were adjusted for multiple comparisons using the Benjamini–Hochberg method. e, Scatterplots of enriched TF motifs in the respective clusters. The y axis shows the enrichment P values from Homer one-sided hypergeometric test of TF motifs and the x axis shows the average gene expression of the corresponding TFs.
