Changes in RNA concentrations in Ad5-infected HFFs determined by RT-PCR

<p><b>Copyright information:</b></p><p>Taken from "Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival"</p><p>Genome Biology 2007;8(4):R58-R58.</p><p>Published online 12 Apr 2007</p><p>PMCID:PMC1896011.</p><p></p> Autoradiograms of products of reverse transcription (RT)-polymerase chain reaction (PCR) amplification of CDC6 RNA isolated from human foreskin fibroblasts (HFFs) infected for the periods indicated. The RNA samples used in experiment 1 were those also used for amplification and hybridization to microarrays, whereas experiments 2 and 3 total RNAs were from two other independent infections of quiescent HFFs. The RT-PCR signals for E2F2 and RHOQ RNAs from the three independent infections were quantified, as described in Materials and methods, zero transformed against the mean of the three zero time point samples included in each experiment, and converted to logvalues for comparison to the changes in concentration of these RNAs determined by hybridization to microarrays. Ad5, adenovirus type 5

Ad5 induced changes of expression of E2F target genes organized by function

<p><b>Copyright information:</b></p><p>Taken from "Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival"</p><p>Genome Biology 2007;8(4):R58-R58.</p><p>Published online 12 Apr 2007</p><p>PMCID:PMC1896011.</p><p></p> E2F target genes, identified by Ren and coworkers [86], were organized by cellular function. Genes significantly regulated by Ad5 (those that pass fold change filter applied previously) are indicated with red/UP or green/DOWN. Grey indicates genes not significantly regulated by Ad5. (Note that none of the 67 E2F target genes were significantly downregulated.

Changes in expression of direct p53 target genes induced by Ad5 infection

<p><b>Copyright information:</b></p><p>Taken from "Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival"</p><p>Genome Biology 2007;8(4):R58-R58.</p><p>Published online 12 Apr 2007</p><p>PMCID:PMC1896011.</p><p></p> The 50 or so genes that are direct p53 targets in human lung fibroblasts [94] are shown clustered based on the changes in their expression observed in adenovirus type 5 (Ad5) infected human foreskin fibroblasts. The column labeled p53 summarizes the p53 induced alterations in expression of these genes, which are listed at the right. Ramps above panels indicate increases in time after infection

Comparison of adenovirus-induced changes in gene expression in HeLa cells and HFFs

<p><b>Copyright information:</b></p><p>Taken from "Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival"</p><p>Genome Biology 2007;8(4):R58-R58.</p><p>Published online 12 Apr 2007</p><p>PMCID:PMC1896011.</p><p></p> The genes reported to exhibit changes in expression at 6 hours or 10 and 21 hours after infection of HeLa cells by adenovirus type 2 (Ad2) [54,55] were isolated from our dataset and clustered on the basis of their responses to infection of human foreskin fibroblasts (HFFs). The changes observed in HeLa cells are summarized in the columns labeled Ad2, in which yellow and blue represent increased and decreased expression respectively. In panel b, the HeLa response is based on the average of the two time points. Ramps above panels indicate increases in time after infection

Kinetic patterns of expression of Ad5-responsive genes and associated cellular functions

<p><b>Copyright information:</b></p><p>Taken from "Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival"</p><p>Genome Biology 2007;8(4):R58-R58.</p><p>Published online 12 Apr 2007</p><p>PMCID:PMC1896011.</p><p></p> The logexpression values of the 2,106 genes that passed the filters described in the text clustered into eight groups are shown at the left, and over-represented Gene Ontology (GO) terms in each cluster at the right. Also shown is a color-bar relating both logratios and fold changes (relative to the average zero values) to color intensity. Ad5, adenovirus type 5