Extended Data Fig. 2. Proportion of interpatient variance explained by MOFA latent factors.

a) Example feature for which a latent factor explains 0% of interpatient variance (here factor 2 explains no variance at all in the expression of gene NCR3—R² = 0). b) Example feature for which a latent factor explains most of the variance (here factor 3 explains 87% of the variance of methylation site cg17731952—R² = 0.87). c) Variance explained by the three histopathological types, each latent factor (LF) independently, predicted total variance explained by all latent factors together if they were completely independent (LF1 to LF4 predicted), and actual variance explained by a model including the four latent factors as covariables (LF1 to LF4 observed). CIMP: CpG island methylator phenotype. d) Typical Total copy number (CN) feature associated with Factor 1. e) Typical Enhancer Methylation feature associated with Factor 2. f) Typical Enhancer Methylation feature associated with Factor 3. g) Typical Gene Body Methylation feature associated with Factor 4. In (a)-(b) and (d)-(g), the gray band corresponds to 95% confidence intervals.

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