Simulated multi-omics data correlation structure for cases 1–3.

Red and “*” mean that features that are simulated with this latent factor are considered signal features. In addition to the existing latent factors and random noise, as shown in the table, additional random noise will be added to all simulated molecular features and phenotype data. The first table is for simulation case 1, where all types of phenotype-specific correlation structures are simulated and considered signal; the second table is for simulation case 2, where only 4-way phenotype-specific correlation structures are simulated and considered signal; the third table is for simulation case 3, where all 3-way, pairwise phenotype-specific correlation structure is simulated and considered signal.