Transcriptional analysis of EBNA3B. (A) Summary of deletions and amino acid changes identified in EBNA3B. Color coding for diseases is the same as in Figure 3A. (B) Summary of nonsense and frameshift mutations identified in EBNA3B. The c.2653dupG and c.2804_2807delCGAA mutations were identified in 2 samples. (C) t-SNE plot illustrating gene expression profiles of LCLs established with WT EBV (gray), EBNA3B-deficient EBV (dEBNA3B, blue), and revertant EBV (orange). (D) Volcano plot comparing gene expression between WT- and dEBNA3B-LCLs. Red circles represent genes with at least one EBNA3B ChIP-seq peak within 100 kb of their transcription start sites. (E) Frequency of EBNA3B ChIP-seq peaks in upregulated and downregulated genes. (F) Gene set enrichment analysis comparing WT- and dEBNA3B-LCLs, highlighting the enrichment of a gene set frequently deleted in glioblastoma (TCGA_GLIOBLASTOMA_COPY_NUMBER_DN). (G) Heat map and dot plots illustrating differential gene expression among the 3 LCLs. Gene symbols highlighted in yellow denote established tumor suppressor genes. (H) Enriched gene set (SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP) identified in WT- and dEBNA3B-LCLs. (I) Gene set enrichment analysis (PTEN_DN.V2_UP) suggesting possible downregulation of the PTEN pathway in dEBNA3B-LCLs. (J) Gene set enrichment analysis (RB_P107_DN.V1_UP) suggesting downregulation of the RB pathway in dEBNA3B-LCLs. FDR, false discovery rate; FWER, family-wise error rate; NES, normalized enrichment score.