Extended Data Fig. 5: Quality control and overview of polar metabolomic and lipidomic data in CBCGA.
a, The distribution of quality control (QC) samples in principal component analysis (PCA) of polar metabolomic data in positive- (left panel) and negative- (right panel) ion modes. b, The distribution of QC samples in PCA of lipidomic data in positive- (left panel) and negative- (right panel) ion modes. c, The numbers and proportions of annotated polar metabolites (top panel) and lipids (bottom panel) in our study. FA, Fatty Acid; GL, Glycerolipid; GP, Glycerophospholipid; SP, Sphingolipid; ST, Sterol Lipids. d, A volcano plot of the 669 annotated polar metabolites (top panel) and 1312 lipids (bottom panel) profiled. Differentially abundant metabolites of different categories were individually color coded. e, Log2 fold change (FC) of different categories of polar metabolites (top panel) and lipids (bottom panel) between tumor and normal tissues. The dashed red line represents the same level of metabolite abundance between the tumor and the normal. Tumor, n = 501 biologically independent samples; Normal, n = 76 biologically independent samples. Center line indicates the median, and bounds of box indicate the 25th and 75th percentiles, the whiskers represent the 1.5× interquartile range. f, A pathway-based analysis of metabolomic changes between tumor and normal tissues. The differential abundance (DA) score captures the average, gross changes for all metabolites in a pathway. A score of 1 indicates that all measured metabolites in the pathway increase in the tumor compared to normal tissues, and a score of −1 indicates that all measured metabolites in a pathway decrease. Pathways with no less than three measured metabolites were used for DA score calculation. Tumor, n = 501 biologically independent samples; Normal, n = 76 biologically independent samples. For d, P values are calculated using the two-sided Kruskal–Wallis test and adjusted by the Benjamini–Hochberg procedure.
