FIG. 1.

Cluster analysis of EBV gene expression after induction of lytic replicative cycle in the presence and absence of SM. (A) Results of simultaneous hybridization to arrays using RNAs from SM-KO cells transfected with different expression plasmids are shown graphically. RNAs were harvested from cells at 0, 6, 12, 24, 48, and 60 h posttransfection. Two RNAs were hybridized to each array to compare global EBV gene expression in the presence or absence of a particular EBV gene. The transfected DNAs representing vector (C), Z, or Z plus SM (Z/SM) and the time of harvest of each RNA are shown below the map. The effect of Z expression on EBV gene expression compared to that of empty vector is therefore represented by the left side of the cluster map. Similarly, the effect of SM plus Z compared to that of Z alone is shown on the right. Two or three independent transfections were performed for each time point. Genes whose expression is increased are in red, those not detectably changed are in black, and those whose expression is decreased are in green. The changes (fold) and other array data for each gene are provided (see Fig. S1 in the supplemental material). (B) SM-dependent genes. Genes whose expression was significantly increased by transfection of SM plus Z compared to transfection of Z alone and whose expression was not significantly increased by Z compared to vector are listed. The gene class of each transcript where clearly established is also listed. All genes not listed as latent or early were either late transcripts or transcripts whose kinetic class has not been formally demonstrated. ORFs in parentheses represent genes that cannot be distinguished by the probe. (C) SM-independent genes. Genes whose expression was significantly increased by transfection of Z alone and whose expression was not significantly increased by transfection of SM plus Z are listed. All genes not listed as late were early lytic transcripts or transcripts whose kinetic class has not been formally demonstrated.