FIG. 3.

Affymetrix microarray profiling of mRNA transcripts in cells containing replicating NNeo/C5B RNA. Shown is an intensity matrix plot (“heat map”) produced by a hierarchical clustering analysis of those oligonucleotide probe sets representing mRNA transcripts identified by two-way ANOVA as being differentially regulated either as a result of cell clone (i.e., clone 2-3 versus clone 3) or the presence or absence of HCV RNA. Microarray analyses were carried out with the Affymetrix HG-U133A GeneChip with total cellular RNA isolated from two different HCV RNA-bearing Huh7 clones—2-3 and 3—and their IFN-treated, clonally related cell progeny (2-3c and 3c). After we eliminated probe sets marked “absent” in HCV-RNA-positive cells and transcripts with a difference in the hybridization intensity signal of <2-fold, the data from 557 probe sets were subjected to clustering analysis. The results demonstrate that the variation between the clone 2-3 and clone 3 Huh7 cell lines influences cellular transcription profiles much more than the presence or absence of replicating HCV RNA.