Genome array analyses: intensity ratios of KSHV latent and lytic genes expressed early during infection of HMVEC-d and HFF cellsa

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  • a HMVEC-d cells were infected with KSHV for 2 and 8 h, and HFF cells were infected for 8 and 24 h. KSHV carrying BCBL-1 cells induced with TPA for 72 h were used as a control for the gene array analyses. Affymetrix analyses of KSHV genes in TPA-induced BCBL-1 cells (control) and infected HMVEC-d and HFF cells described in the legend for 4A were used to calculate the intensity ratios of expressed genes and to construct the table. The normalized infected Cy-3/ uninfected Cy-5 expression intensity ratios were used to construct the cluster diagrams. Intensity ratios closer to 1.0 and below were taken as an indication of nonexpressed genes, and intensity ratios less than 2.0 and below were considered as nonsignificant expression. KSHV genes were categorized as per Jenner et al. (22) and color coded to represent the latency and lytic cycle-associated genes as described for Fig. 4. Green, latency-associated genes; blue, purple, and orange; primary, secondary, and tertiary lytic genes, respectively; white, uncharacterized.