Figure 4

Differentially expression analysis and pathway enrichment analysis of genes in EBV-positive DLBCL cells treated with IL-21. (a, b) EBV-positive DLBCL primary cells and Farage cells were treated with IL-21 (100 ng/mL for 48 h) or left untreated and gene expression was analysed by RNA-seq. MA plots show the displayed A values (average log2 transformed expression value) and M values (fold change in the log2 transformed expression value) of the data from Farage cells and the primary cells. The red dots indicate differentially expressed genes (DEGs) that were upregulated (fold-change > 1.5, q values < 0.01). The blue dots indicate DEGs that were downregulated (fold-change < − 1.5, q values < 0.01). The grey dots represent genes that were not differentially expressed. (c) Unsupervised hierarchical clustering of expression fold change data for differentially expressed disease-associated genes (fold-change > 1.5 or < − 1.5, q values < 0.01) in the primary and Farage cells. Each group is comprised of three pooled biological replicates. (d, e) Top-ranked pathways enriched in the differentially expressed genes (DEGs) in KEGG pathway analysis. The colours indicate the q-values (high: white, low: blue). Lower q-values indicate more significant enrichment. The dot size reflects the number of DEGs (larger dots indicate a larger number). ”Rich Factor” indicates the value of the enrichment factor, which is the quotient of the foreground value (the number of DEGs) and the background value (the total number of genes). The larger the value, the more significant is the enrichment. Boxed text indicates common top-ranked pathways in the primary cells and Farage cells.