Extended Data Fig. 4: Validation of BAP1 mutation-specific metabolite changes in CPTAC and CPTAC_val datasets.
From: UnitedMet harnesses RNA–metabolite covariation to impute metabolite levels in clinical samples
a) UnitedMet’s predicted metabolite differences between BAP1-mutant and wildtype samples align with measured data in CPTAC and CPTAC_val. Differential abundances of imputed metabolites between BAP1-mutant and wildtype samples in TCGA KIRC were compared to ground-truth differences in the measured CPTAC (left) and CPTAC_val (right) cohorts. Metabolites in dark blue are consistently and significantly enriched/depleted (FDR-adjusted p < 0.1, two-sided Wilcoxon rank-sum test) in both measured and predicted cohorts. b) Measured metabolite level changes in BAP1 mutant v.s. BAP1 wildtype samples in CPTAC (top, MUT, n = 8 patient samples; WT, n = 42 patient samples) and CPTAC_val (bottom, MUT, n = 6 patient samples; WT, n = 50 patient samples) dataset. Boxplots comparing measured unphosphorylated glucose, citrate, fumarate, and malate levels in MUT BAP1 v.s. WT BAP1 samples. p values are calculated by unpaired two tailed parametric t-tests. In the box plots, the center line represents the median, the bounds of the box indicate the interquartile range (25th to 75th percentiles), and the whiskers extend to 1.5 times the interquartile range. Individual data points are shown as dots.
