Fig 1: Random forest selection of potential core targets for sodium dehydroacetate (Na‐DHA) interference in bone metabolism and expression validation. (A) Gene importance ranking based on “Mean Decrease Accuracy”. The x‐axis represents the mean decrease accuracy value, and the y‐axis represents the genes. Larger values indicate a greater contribution of the gene to distinguishing between the “Na‐DHA treatment group” and the “control group” in the model. (B) Gene importance ranking based on “Mean Decrease Gini”. The x‐axis represents the mean decrease Gini value, and the y‐axis represents the genes. Larger values indicate the critical role of the gene in decision tree node splitting (differentiating sample groups). (C) Cross‐validation error curve of the random forest model. The x‐axis represents the number of features (genes) included, and the y‐axis represents the cross‐validation error. The curve decreases as the number of features increases, suggesting that the core target subset improves the model's generalization ability. (D) Venn diagram showing the intersection of core targets identified by the “Mean Decrease Accuracy” and “Mean Decrease Gini” methods. The intersecting genes (LCMT1, ARHGEF11, CAT, VCAM1) are the key targets identified by both methods. (E) Violin plot showing the expression distribution differences of core targets between the osteoporosis‐related group (red, Osteoblast group) and the control group (blue, Osteoarthritis group). The y‐axis represents gene expression levels, and the distribution and dispersion reflect the statistical significance of expression differences between groups (adj p < 0.05).
Fig 2: Molecular docking results of core targets with Na‐DHA. (A) Molecular docking between LCMT1 and Na‐DHA. The left side shows the overall structure of LCMT1 protein (surface transparency displayed), and the right side shows an enlarged view of the binding region. Na‐DHA (cyan) forms hydrogen bonds with the Lys37 and Arg73 residues of LCMT1 (yellow dashed lines indicate hydrogen bond distances). (B) Molecular docking between ARHGEF11 and Na‐DHA. The left side shows the overall structure of ARHGEF11 protein, and the right side shows an enlarged view of the binding region. Na‐DHA (green) forms a hydrogen bond with the Ser123 residue of ARHGEF11. (C) Molecular docking between VCAM1 and Na‐DHA. The left side shows the overall structure of VCAM1 protein, and the right side shows an enlarged view of the binding region. Na‐DHA (yellow) forms a hydrogen bond with the Ile68 residue of VCAM1.
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