Identification of shared oxidative stress related hub genes in NAFLD and atherosclerosis using bioinformatics and machine learning

Figures

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  Fig. 1. The simplified analysis workflow of this research. The abbreviations in Fig. 1 are as follows: Non-alcoholic fatty liver disease (NAFLD), Atherosclerosis (AS), Common Differentially Expressed Genes (Co-DEGs), Protein–Protein Interaction (PPI), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine (SVM), Receiver Operating Characteristic (ROC), Decision Curve Analysis (DCA).

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  Fig. 2. Identification of Co-DEGs between NAFLD and AS. (A) Volcano plot of DEGs in AS; (B) Volcanic plot of DEGs in NAFLD; (C) Venn diagram of upregulated Co-DEGs in AS and NAFLD; (D) Venn diagram of downregulated Co-DEGs in AS and NAFLD.

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  Fig. 3. The 20 Co-DEGs between NAFLD and AS. (A) Heatmap of Co-DEGs in AS; (B) Heatmap of Co-DEGs in NAFLD; (C) The PPI network of Co-DEGs.

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  Fig. 4. Functional Enrichment Analysis. (A) GO enrichment analysis; (B) KEGG enrichment analysis.

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  Fig. 5. Screening of Co-expressed Oxidative Stress-related Hub Genes Through Machine Learning Techniques. (A, E) Lasso cross validation diagram in AS and NAFLD; (B, F) Lasso coefficient analysis diagram in AS and NAFLD; (C, G) Accuracy of feature variables based on SVM method in AS and NAFLD; (D, H) Error of feature variables based on SVM method in AS and NAFLD; (I) Venn diagram of screening hub genes through machine learning methods.

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  Fig. 6. Diagnostic Value of ADM and IL2RB in NAFLD and AS and Construction of TF-mRNA Regulatory Network. (A) The ROC curves of hub gene ADM and IL2RB in AS; (B) The ROC curves of hub gene ADM and IL2RB in NAFLD; (C) TF-mRNA regulatory network.

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  Fig. 7. Construction of the Nomogram Model and Evaluation of Diagnostic Value in the AS training set and validation set. (A) The nomogram model in the AS training set; (B, E) The calibration curves of nomogram model in the AS training set and validation set; (C, F) The DCA curves of nomogram model in the AS training set and validation set; (D, G) The ROC curves of nomogram model in the AS training set and validation set.

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  Fig. 8. Construction of the Nomogram Model and Evaluation of Diagnostic Value in the NAFLD training set and validation set. (A) The nomogram model in the NAFLD training set; (B, E) The calibration curves of nomogram model in the NAFLD training set and validation set; (C, F) The DCA curves of nomogram model in the NAFLD training set and validation set; (D, G) The ROC curves of nomogram model in the NAFLD training set and validation set.

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  Fig. 9. Outcomes of Immune-Related Cells Infiltration Assessment. (A) Immune-Related Cells Infiltration in AS; (B) Immune-Related Cells Infiltration in NAFLD.