Table 1.
GEO microarray chip information.
Fig 1.
Flow chart for the comprehensive analysis of PRDEGs. t-MN, therapy-related myeloid neoplasm; GSEA, gene set enrichment analysis; DEGs, differentially expressed genes; PRGs, pyroptosis-related genes; KEGG, Kyoto Encyclopedia of Genes and Genomes; GO, Gene Ontology; PRDEGs, pyroptosis-related differentially expressed genes; PPI, protein–protein interaction; TF, transcription factor; ROC, receiver operating characteristic; DiffBoxplot, differential boxplot.
Fig 2.
Differential gene expression analysis.
A. Differential gene expression analysis using a volcano map of the t-MN and control samples in the integrated GEO dataset (combined GEO dataset). B. Venn diagram of DEGs and PRGs in the combined GEO dataset. C. Heat map of PRDEGs in the combined GEO dataset. t-MN, therapy-related myeloid neoplasm; DEGs, differentially expressed genes; PRGs, pyroptosis-related genes; PRDEGs, pyroptosis-related differentially expressed genes. In the heat map, orange represents the t-MN sample, whereas dark blue denotes the control sample. High expression is indicated in red, whereas low expression is represented in purple.
Table 2.
Results of GO and KEGG pathway enrichment analyses for PRDEGs.
Fig 3.
GO and KEGG pathway enrichment analyses of PRDEGs.
A. The results of GO and KEGG pathway enrichment analyses for PRDEGs related to pyroptosis are shown. Ordinates represent GO and KEGG terms. B–E. The results of GO and KEGG pathway enrichment analyses for PRDEGs related to focal death are shown in the network diagram: BP (B), CC (C), MF (D), and KEGG (E). Blue nodes represent entries, orange nodes represent molecules, and lines represent the relationships between entries and molecules. PRDEGs, pyroptosis-related differentially expressed genes; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; BP, biological process; CC, cellular component; MF, molecular function. In the bubble diagram, the bubble size represents the number of genes, whereas the bubble color reflects the adjusted p value. A redder hue indicates a smaller adjusted p value, whereas a purple hue indicates a larger adjusted p value. The screening criteria for the GO and KEGG pathway enrichment analyses were adjusted p < 0.05 and FDR value (q) < 0.25.
Table 3.
Results of GSEA for the combined GEO dataset.
Fig 4.
GSEA for the combined GEO dataset.
A. Six biological function mountain maps of GSEA for the combined GEO dataset. B–G. Gene set enrichment analysis (GSEA) showed significant enrichment of genes within several key pathways, including the PI3K-Akt signaling pathway (B), PI3K-Akt signaling in cancer (C), Notch pathway (D), FCGR3A-mediated IL10 synthesis (E), signaling by NOTCH4 (F), and Wnt signaling pathway (G). t-MN, therapy-related myeloid neoplasm; GSEA, gene set enrichment analysis. The screening criteria for GSEA were adjusted p < 0.05 and FDR (q) < 0.25.
Fig 5.
PPI network and hub gene analysis.
A–B. PPI network of PRDEGs. STRING interaction network diagram (A), Cytoscape interaction network diagram (B). C–G. PPI network calculated by five algorithms of the cytoHubba plugin: MCC (C), MNC (D), degree (E), EPC (F), and closeness (G). H. Venn diagram shows the intersection of the top 10 PRDEGs from the five algorithms of the cytoHubba plugin. PRDEGs, pyroptosis related differentially expressed genes; t-MN, therapy-related myeloid neoplasm; PPI, protein–protein interaction.
Fig 6.
Regulatory network of hub genes.
A. The mRNA-TF regulatory network of focal death-related differential genes (DEGs). B. mRNA-miRNA regulatory network of PRDEGs. TF, transcription factor. Orange represents the mRNA, green represents the TF, and purple represents the miRNA.
Fig 7.
Differential expression validation and ROC curve analysis.
A. Grouping comparison diagram of hub genes in the t-MN and control samples in the combined GEO dataset. B–D. ROC curve analysis of hub genes Trp53, Cybb (B); Foxo3, Mtor (C); and Gpx3 (D) from the combined GEO dataset. * represents p < 0.05, which is statistically significant. t-MN, therapy-related myeloid neoplasm; ROC, receiver operating characteristic; AUC, area under the curve; TPR, true positive rate; FPR, false positive rate. Dark blue and orange denote the control and t-MN samples, respectively.
Fig 8.
Immune infiltration analysis using the CIBERSORT algorithm in the combined GEO dataset.
A–B. Bar chart (A) and group comparison chart (B) of the proportion of immune cells in the integrated GEO dataset (combined GEO dataset). C. Correlation heat map of the abundance of immune cell infiltration in the combined GEO dataset. D. Bubble map of correlation between hub genes and the abundance of immune cell infiltration in the combined GEO dataset. t-MN, therapy-related myeloid neoplasm. * represents p < 0.05, which has statistical significance. The absolute value of the correlation coefficient (r) is categorized as follows: a value below 0.3 indicates weak or no correlation, values between 0.3 and 0.5 signify weak correlation, values between 0.5 and 0.8 represent moderate correlation, and values above 0.8 indicate strong correlation. The t-MN samples are shown in orange, whereas the control samples are denoted in dark blue. In correlation visualizations, purple indicates negative correlation, and red signifies positive correlation, with the intensity of the color indicating the strength of the correlation.