Fig 2: Potential VHL substrates with clinical prognostic significance. (A) Venn diagram showing the overlap between the two protein lists. (B) Kaplan–Meier analysis for the expression score of the 57-gene signature in relationship with overall survival, progression-free survival and disease-free survival of the TCGA ccRCC patients. p values calculated based on Cox regression analysis. (C) mRNA expression score of the 57-gene signature in matched primary ccRCC tumors and pulmonary metastases (GSE85258). p value calculated by t test. (D) Protein expression score of the 57-protein signature in the ccRCC CPTAC patient tumors and NAT tissues, stratified based on chromosome 3p status. *** p < 0.01,**** p < 0.001, ns (not significant, p > 0.05), calculated by t test. (E) Western blot of TGFBI in 786-O-Ctrl and 786-O-VHL cells. (F) The MS/MS result of the TGFBI peptide LAPVYQKubLLER containing the ubiquitinated lysine K676, the Δm between y5 and y4 corresponds to the mass of Lys residue plus diGly. (G) TGFBI protein expression in normal tissues and tumors in ccRCC patients based on the CPTAC data. (H) Kaplan–Meier analysis for overall survival for patients of the TCGA ccRCC cohorts based on TGFBI mRNA expression. p value calculated from Cox regression analysis. (I) Western blot of NFKB2/p100 in 786-O-Ctrl and 786-O-VHL cells. (J) The MS/MS result of the NFKB2 peptide YGCEGPSHGGLPGASSEKubG containing the ubiquitinated lysine K72 and GHTPLDLTCSTKubVK containing K741. (K) NFKB2 protein expression in normal tissues and tumors in ccRCC patients based on the CPTAC data. (L) Kaplan–Meier analysis for overall survival for patients of the TCGA ccRCC cohorts based on NFKB2 mRNA expression. p value calculated from Cox regression analysis. (M) Western blot of TGFBI and NFKB2/p100 in RCC4-Ctrl, RCC4-VHL, RCC10-Ctrl and RCC10-VHL cells.