Transcriptional regulation of EBV gene expression demonstrates diversity of latency types. (A) Gene expression is shown as read counts per million reads aligned (y-axis) at canonical type I latency genes EBER1, EBER2, and EBNA1. Rows show individual samples and are colored alternating red/blue to emphasize sample-track pairing. (B) Immunogenic viral genes associated with type II and III latency are also expressed, such as LMP1. (C) EBV gene expression is highly diverse across ARL samples. The heatmap shows gene expression profiles of latency-associated genes (y-axis) across samples (x-axis). Gene expression is in units of RPKM normalized by fraction of reads aligning to EBV (“Methods”). (D) Genes associated with lytic reactivation, such as transcripts at the BamHI H locus, were expressed in primary ARL tumor samples. (E) Immunohistochemical staining for viral proteins EBNA2 and LMP1 was used to classify viral gene expression latency in ARL cases. A BL sample with latency I (upper) and a DLBCL sample with latency III (lower) are representative examples. A complete analysis can be found in Table 2.