Fig. 2: Analysis of tumor cell heterogeneity between Zbp1^−/− and WT groups.

A Thirteen major cell types were identified using the Seurat R package and visualized by UMAP. B Tumor cells in Zbp1^−/− and WT groups were identified using CopyKAT. C The KEGG enrichment analysis was conducted on the upregulated DEGs in tumor cells from the Zbp1^−/− group. The left panel presents a KEGG cnetplot illustrating the associations between enriched pathways (category nodes) and their corresponding DEGs (gene nodes). The size of each node reflects the number of DEGs involved in the respective pathway, while the node color denotes the adjusted p-value. The right panel displays a KEGG dotplot of the same dataset, where the x-axis represents the GeneRatio. The size of each bubble indicates the number of DEGs, and the bubble color signifies the adjusted p-value. D The KEGG enrichment analysis of downregulated DEGs in tumor cells from the Zbp1^−/− group is presented. The left panel displays a KEGG cnetplot, maintaining consistent node size and color coding as depicted in panel (C). The right panel features a KEGG dotplot, preserving the same axis, size, and color coding as in panel (C). KEGG enrichment analyses were conducted independently for upregulated and downregulated differentially expressed genes (DEGs), with pathways deemed significant at at adjusted p < 0.05. The GeneRatio represents the proportion of DEGs associated with each pathway. Given the variation in the total number of DEGs between the two groups, the GeneRatio and node sizes are comparable solely within each respective group. E GSVA enrichment analysis of Hallmark pathways for differentially expressed genes between tumor cells in Zbp1^−/− and WT groups. F, G GSEA analyses reveal differences in KEGG and GO pathway enrichment between tumor cells from Zbp1^−/− and WT mice. Pathways were considered significant if they exhibited an absolute normalized enrichment score (|NES | ) greater than 1, a nominal p-value less than 0.05, and an adjusted p-value (false discovery rate, FDR) below 0.25. The top 10 upregulated pathways (depicted in the left panel) and the top 10 downregulated pathways (depicted in the right panel) were selected based on their NES values. The X-axis represents the rank of genes within the ordered dataset, determined by log₂ fold change. The Y-axis in the upper panel illustrates the Running Enrichment Score (ES) for each pathway, while the Y-axis in the lower panel displays the ranked list metric, specifically the log₂ fold change, for each gene. H Regulatory specificity scores (RSS) of the top five transcription factors differ between Zbp1^−/− and WT groups. Regulons were ranked by rss within each group (y-axis: rss; x-axis: rank). Filtering thresholds (zThreshold=0.3, thr = 0.01) were applied, and top-ranked regulons are annotated. I Comparison of regulon activities between WT and Zbp1^−/− groups. Each violin represents the density distribution of single-cell AUC values, with an embedded boxplot indicating the median and interquartile range. Individual dots represent outlier cells outside 1.5 × IQR. Statistical significance between WT and Zbp1^−/− groups was assessed using the Wilcoxon rank-sum test; corresponding p-values are shown above each panel.