Fig. 2

Proteomic pathway-based classifier. A Heatmap of 28 overlapping proteins that were significantly differentially expressed between tumor and adjacent benign samples (B-H adjusted P-value < 0.05, fold change > 2 or < 0.5), and 4 clusters (cluster 2, 5, 8, 10 in Additional file 2: Figure S1B) from mFuzz analysis (one-way ANOVA, B-H adjusted P-value < 0.05). Proteins that exhibit an increasing trend with ISUP grades are indicated by the color red, while those with a decreasing trend are represented by blue. Proteins that were not detected in our dataset are denoted by gray. Different shapes reflects the diverse biological functions of the proteins. B The protein–protein interaction network of the 28 proteins from STRING. C An unsupervised classifier based on proteomic pathways. D–E The t-SNE shows the distribution of all tumor samples using ISUP standard and the pathway-based classifier. The classifier was based on the selected 13 proteins shown in Fig. 2A. F The overlay of proteomic pathway-based subtypes using the ISUP classification standard for PCa