Fig. 1: MOFA of whole genomes, transcriptomes and methylomes of the MESOMICS cohort (n = 120).
a, Proportion of interpatient variance within a molecular layer explained by WHO-defined histopathological type (left) and MOFA latent factors 1–4 (right). For example, 7% of variation present in RNA expression can be explained by mesothelioma types, in contrast with 20% explained by integrative MOFA. CN, segmental copy number; DNA alt, rearrangements and mutations; MethBod, DNA methylation level at body regions; MethEnh, DNA methylation level at enhancer regions; MethPro, DNA methylation level at promoter regions; RNA, gene expression level. b, Network of the correlations between latent factors, tumor histopathology and previously published molecular scores. The arc colors, widths and transparency correspond to Pearson correlation coefficients. Features uncorrelated with any other features are highlighted in bold. AI, artificial intelligence; C/V ratio, log2 ratio of CLDN15 to VIM gene expression; S score, sarcomatoid gene expression score; E score, epithelioid gene expression score. c, Interpretation of MOFA latent factors. Plus signs indicate positive correlations and minus signs indicate negative correlations. d, Correlation between the ploidy factor (LF1) and ploidy. e, Correlation between the CIMP factor (LF4) and CIMP index. The samples are colored by histological type. f, Forest plot of the hazard ratios of MOFA latent factors for overall survival. The squares correspond to estimated hazard ratios and the segments correspond to their 95% confidence intervals. In b–e, P values, q values and r coefficients were determined by two-sided Pearson correlation tests. In d and e, the gray bands represent 95% confidence intervals.
