Fig. 3

Characterization of metabolomics between HCT and DNT. (A) Plot of PCA scores between the two groups. After conducting dimension analysis, the reduced samples were plotted as relative coordinate points on the principal components p1 and p2. The distance between each point reflects the level of aggregation and dispersion among samples, with shorter distances indicating higher similarity and longer distances suggesting greater dissimilarity. (B) Plot of PLS-DA scores between the two groups. The PLS-DA score plot is commonly used to visually demonstrate the model’s classification effectiveness, where a larger separation between the two sample groups indicates a more pronounced classification effect. (C) PLS-DA permutation test plot. The abscissa represents the permutation retention of the test, while the ordinate represents R² (red dot) and Q² (blue triangle) values. The dashed lines correspond to regression lines for R² and Q² respectively. Notably, the regression line for R² is positioned above that of Q². Moreover, the intercept between the regression line for Q² and y-axis is -0.0926, indicating a well-fitted model with high predictability suitable for subsequent data analysis. (D) Volcano plot of differentially expressed metabolites. The horizontal axis represents the log₂FC in expression between the two groups, while the vertical axis represents the -log10(p-value) of statistical test for metabolite expression difference. Higher values indicate greater significance in expression differences. Each dot on the plot corresponds to a specific metabolite, with dot size indicating VIP value. Red dots represent up-regulated metabolites, blue dots represent down-regulated metabolites, and gray dots represent non-differential metabolites. The position of each dot reflects its level of significance in terms of expression difference