Fig. 2: Integrative view on functional and molecular profiles of pan-cancer MSE samples.

a Schematic depiction of the multi-omics factor analysis (MOFA) workflow. b Percentage of variance explained by each data type per factor, for the first seven factors ranked by highest overall fraction of variance explained. c Heatmap showing the top features contributing to the first seven MOFA factors for each of the 149 MSE samples. For each of the top seven MOFA factors, the values of the features that contribute most to this factor are shown. Sample type, tumor type, data type, and select feature names are annotated. d Correlation of factor 1 with either (top panel) EPCAM expression (excluding non-epithelial tumors; n = 116) or (bottom panel) expression of immune-marker PTPRC/CD45 (n = 131 samples). Linear regression line with 95% confidence bands, R squared, and corresponding P value (two-sided t test) are indicated. e Cell type composition per sample. Samples are grouped into 8 clusters based on their composition using hierarchical clustering (pearson correlation, complete linkage) and tree-cutting. f Example PCY images of MSE samples from each cluster. Images represent 8 out of 150 biological replicates, with 400 images of DMSO-treated cells per sample. Stainings and scale bars are indicated.