Fig. 4

MOFA+ integrates a multi-modal mouse gastrulation atlas to reveal epigenetic signatures associated with lineage commitment. a, b Characterization of Factor 1 as ExE endoderm formation and Factor 2 as Mesoderm commitment. Top left plot shows the percentage of variance explained by the Factor across the different views (rows) and groups (embryonic stages, as columns). Bottom left plot shows the distribution of Factor values for each stage, colored by cell type assignment. Histograms display the distribution of DNA methylation and chromatin accessibility weights for promoters and enhancer elements. c Dimensionality reduction using t-SNE on the inferred MOFA factors. Cells are colored by cell type. d Same as (c), but cells are colored by Factor 1 values (top left) and Factor 2 values (bottom left); by the DNA methylation levels of the enhancers with the largest weight in Factor 1 (top middle) and Factor 2 (bottom middle); by the chromatin accessibility levels of the enhancers with the largest weight in Factor 1 (top right) and Factor 2 (bottom right)