Fig. 3

MOFA+ reveals context-dependent DNA methylation signatures associated with cellular diversity in the mammalian cortex. a Percentage of variance explained for each Factor across the different groups (cortical layer, x-axis) and views (genomic context, y-axis). For simplicity, only the first three factors are shown. b, c Characterization of (b) Factor 1 as the two major neuron populations and (c) Factor 3 as increased cellular diversity of excitatory neurons in deep cortical layers. The beeswarm plots show the distribution of Factor values for each group, defined as the neuron’s cortical layer. In the left plot, cells are colored by neuron class. In the middle and right plots, the cells are colored by average mCG and mCH levels (%), respectively, of the top 100 enhancers with the largest weights. d UMAP projection of the MOFA factors. Each dot represents a cell, colored by maximally resolved cell type assignments. e Correlation of enhancer mCG weights (x-axis) and mCH weights (y-axis) for Factor 1 (top) and Factor 3 (bottom)