Fig. 4

Reproducibility of molecular tumor classes on the level of protein profiles. The heatmaps show for each molecular tumor classification and all histotypes the degree with which a molecular class is distinguishable from other classes based on protein profiles. Blank matrix entries indicate fewer than five cases which were excluded from the analysis. In the classification by Ciriello et al., gynecological cancers (breast, uterine and ovarian) show highest protein-level effects of genetic classes, whereas the molecular classes based on Heim et al. have less impact on proteins overall. The genetic complexity reduction classification has relatively distinct protein profiles for histological tumor types. Hoadley et al. propose classes well discriminable by protein profile (however, due to the high agreement with histotypes, only a few classes contain sufficient cases to evaluate protein level effects)