DE gene analysis among human CD34⁺ stem cells treated with IFN-γ compared with that of the control group reveals distinct genes and pathways affected by inflammation. (A) The principal component analysis was performed with all the samples, and the first 2 principal components are plotted. Data show clear separation of treated (n = 3) and nontreated samples (n = 3) into 2 distinct groups. (B) The DE analysis results are plotted as a volcano plot. x-axis shows log2FC, and y-axis shows −log10 (P value) for each gene. Each dot represents a gene and the colors indicate significance level. (C) Genes that are significant by log2 fold change (log2FC) > 2 and false discovery rate (FDR) < 0.05 are plotted in the heat map. (D) Genes involved in B-cell activation and early development are differentially expressed between treated and nontreated groups. (E) Overrepresentation analysis shows significant pathway hits (FDR < 0.05) for 704 DE genes. Size of the circle represents the number of genes in each pathway; color represents the significance level. (F) Gene set enrichment analysis identifies 3 significant pathways based on the enrichment score (top). The value of the ranking metric is shown along the list of the ranked genes (bottom).