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. 2023 Dec 8;7:131. doi: 10.1038/s41698-023-00479-5

Fig. 3. Subtype-specific signatures determined by ALLIUM.

Fig. 3

Cross-decomposition analysis with Partial Least Squares (PLS) Canonical analysis. The UMAP plots indicate components 1 and 2 for a the DNAm (n = 167,353) vs the GEX (n = 19,774) unselected signatures, and b the ALLIUM DNAm (n = 379) and GEX (n = 356) signatures (right). The points indicate the training (67%, blue) and test sets (33%, red). The Pearson’s correlation coefficient for the comparing modalities per component is denoted in the title of each plot. Boxplots demonstrating the c GEX levels for four selected genes across 315 patients grouped by revised molecular subtype. d DNAm levels for four selected CpG sites across 1125 patients by revised molecular subtype. The boxes are color-coded by respective subtype according to the key at the bottom of the panel. The Benjamini-Hochberg (BH) corrected Kruskal-Wallis H-test p value indicates the statistical significance between subtypes (bottom right). Asterisks indicate the subtype(s) for which ALLIUM chose each specific CpG or GEX signature. The lines (whiskers) on the boxplots represent the distribution of residual data points beyond the lower and upper quartiles.