Fig. 2

Protein associations with genomic, transcriptomic, and pathological hallmarks of mpMRI visibility. A Protein-coding RNAs (left) and proteins (right) associated with hallmarks of mpMRI visibility, colored by positive (orange) or negative (purple) associations. Top barplot shows the number of hallmarks each RNA or protein was associated with. Side barplot shows the number of validated RNAs or proteins associated with each hallmark (Additional file 1: Methods). Bottom covariate bar indicates significant RNAs or proteins associated with visible (green) or invisible (black) tumors (FDR < 0.05). B Genes that were associated with three or more hallmarks or mpMRI visibility at the protein level. Left barplot shows the number of hallmarks each gene is associated with at the RNA (pink) or protein (blue) level. Dot maps show the effect size of the association between gene expression and each hallmark. The size of the dot represents the magnitude of the effect, the color denotes the direction (positive: orange; negative: purple), and background shading the FDR. Only significant associations have a gray background. Right barplot shows the log₂ fold change between mpMRI-visible and invisible tumors for RNA and protein. C Spearman’s correlation between tumor protein/PGA and protein/mpMRI visibility associations. Validated proteins with abundance significantly correlated with PGA (FDR < 0.2) are colored in black. D Summary of the correlation between associations with each hallmark and mpMRI visibility in protein-coding RNAs and proteins. E A 3-protein model classified mpMRI-visible tumors with an area under the curve (AUC) of 88%. AUC confidence intervals in parentheses and shaded in blue. Inset: The protein signature was associated with worse biochemical recurrence (BCR)-free survival in an independent cohort (n = 76 patients) [11]. Low: n = 49, 20 events; High: n = 26, 15 events. PGA: proportion of the genome with a copy number abberation; IDC/CA: intraductal carcinoma or cribriform architecture; mpMRI: multiparametric magnetic resonance imaging; FDR: false discovery rate; ρ: Spearman’s rho; FC: fold change; HR: hazard ratio