Table 1.
Current observational studies on Alzheimer’s disease (AD) and osteoarthritis (OA).
Fig 1.
AD: alzheimer’s disease; OA: osteoarthritis; Co-DEGs: common differentially expressed genes; GO: gene ontology; KEGG: kyoto encyclopedia of genes and genomes; PPI: protein-protein interaction; ROC: receiver operating characteristic; GSEA: gene set enrichment analysis; GSVA: single-gene genome variation analysis.
Fig 2.
Sample distribution principal component analysis (PCA) plot.
PCA plot of sample distribution before (A) and after (B) of the AD-related training set. PCA plot of sample distribution before (C) and after (D) of the OA-related training set.
Fig 3.
Differential expression analysis.
Gene expression in the AD training group (A) and OA training group (B) between disease samples and normal samples. (C) The overlap of upregulated DEGs in AD and OA training sets. (D) The overlap of downregulated DEGs in AD and OA training sets.
Table 2.
Basic information and grouping of GEO data set.
Fig 4.
Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted on common DEGs (Co-DEGs) shared between AD and OA.
(A) GO enrichment analysis of Co-DEGs. The x-axis represents the gene ratio (the proportion of DEGs in the GO term relative to the total), the y-axis represents the GO terms ordered by enrichment significance (with color scale indicating the significance level), and the size of the circles represents the number of enriched genes in each term. (B) KEGG enrichment analysis of Co-DEGs, with the x-axis showing the number of enriched genes and the y-axis represents the different KEGG pathways.
Fig 5.
Protein-Protein Interaction (PPI) network.
(A) PPI network of Co-DEGs. (B) Cytoscape v.3.8.0 facilitates the visualization of PPI networks. Green represents down-regulated Co-DEGs, while red represents up-regulated Co-DEGs. (C) PPI network of Co-DEGs in the degree algorithm; the color of the circles in the fig from yellow to red represents the gradual increase in the score.
Fig 6.
The top 10 CO-DEGs were identified based on their degree in the dataset.
(A) Expression of the 10 core genes in the validation set of AD. (B) Expression of the 10 core genes in the validation set of OA. *P <0.05, **P < 0.01, ***P< 0.001.
Fig 7.
(A-B) Receiver Operating Characteristic (ROC) curves and model performance for significantly differentially expressed core genes (EFEMP2, GABARAPL1, TSPO) in AD validation. (C) Violin plot of EFEMP2, GABARAPL1, TSPO expression in AD validation. (D-E) ROC curves and model performance for EFEMP2, GABARAPL1, TSPO in OA validation. (F) Violin plot of EFEMP2, GABARAPL1, TSPO expression in OA validation.
Fig 8.
Gene set enrichment analysis (GSEA) of EFEMP2 in AD.
y-axis: The "Running Enrichment Score" reflects the enrichment level of the EFEMP2, GABARAPL1, and TSPO gene sets in AD. The "Ranked List Metric" displays the ranking of genes within the dataset. x-axis: Represents the position of genes in the sorted dataset.
Fig 9.
Gene set enrichment analysis (GSEA) of GABARAPL1 in AD.
y-axis: The "Running Enrichment Score" reflects the enrichment level of the EFEMP2, GABARAPL1, and TSPO gene sets in AD. The "Ranked List Metric" displays the ranking of genes within the dataset. x-axis: Represents the position of genes in the sorted dataset.
Fig 10.
Gene set enrichment analysis (GSEA) of TSPO in AD.
y-axis: The "Running Enrichment Score" reflects the enrichment level of the EFEMP2, GABARAPL1, and TSPO gene sets in AD. The "Ranked List Metric" displays the ranking of genes within the dataset. x-axis: Represents the position of genes in the sorted dataset.
Fig 11.
y-axis: The "Running Enrichment Score" reflects the enrichment level of the EFEMP2, GABARAPL1, and TSPO gene sets in OA. The "Ranked List Metric" displays the ranking of genes within the dataset. x-axis: Represents the position of genes in the sorted dataset.
Fig 12.
y-axis: The "Running Enrichment Score" reflects the enrichment level of the EFEMP2, GABARAPL1, and TSPO gene sets in OA. The "Ranked List Metric" displays the ranking of genes within the dataset. x-axis: Represents the position of genes in the sorted dataset.
Fig 13.
y-axis: The "Running Enrichment Score" reflects the enrichment level of the EFEMP2, GABARAPL1, and TSPO gene sets in OA. The "Ranked List Metric" displays the ranking of genes within the dataset. x-axis: Represents the position of genes in the sorted dataset.