Fig. 3

Analysis of metabolite-gene (MG) pairs from metabolite-gene-pathway sets (MGPs) predicted for the 16 AML samples and 20 RCC samples. a Number of MGPs predicted for the seven mutated genes from the 16 AML samples. It should be noted that samples having IDH1 or IDH2 mutation were also considered together, presented as “IDH,” in order to examine the overall effects of mutations in IDH1 and IDH2. b Classification of the detected peaks from relative quantification of metabolites from the 17 AML samples. c AUC values of target metabolites from the final six MGPs, which were predicted from the computational workflow and supported with the AML metabolome data (Fig. 1). AUC values of target metabolites were predicted using MetaboAnalyst [33]. The black dashed line indicates the AUC value of 0.7. d AUC values for target metabolites from the final six MGPs (red dots) and 60 metabolites from the AML metabolome data; these 60 metabolites include those not predicted as a target metabolite for MGPs and are paired with each of the presented target genes (box plots). These 60 metabolites correspond to the peaks in the metabolome data that are annotated, and also present in the GEMs in b. e–h Same analyses (a–d) conducted for the 21 RCC samples. In e, MGPs were predicted for the six mutated genes from the 20 RCC samples. Samples having NOTCH1 or NOTCH2 mutation were considered together as “NOTCH,” and samples having ERBB2, ERBB3, or ERBB4 mutation were considered together as “ERBB” in order to collect the sufficient number of samples to generate AUC values. In h, AUC values for target metabolites from the final 15 MGPs (red dots) and 104 metabolites from the RCC metabolome data are presented. These 104 metabolites include those not predicted as a target metabolite for MGPs and are paired with each of the presented target genes (box plots)