Figure 2

Mapping of differentially expressed genes onto Volcano and MA plots. Genes significantly regulated by E1A and found to be up-regulated or down-regulated by BAM analysis are highlighted in red or green, respectively, while the non-regulated genes are shown in grey. The top 50 regulated genes (up or down) from Table 1 are named along with a few un-annotated genes called Rik identifiers. Left panel: volcano plot of absolute BAM Zcut values plotted versus log-fold-change-ratios on a log-equivalent transformed scale, denoted M = glog(S/Q), where (S) denotes cells with E1A and (Q) without E1A. Right panel: MA plot. Vertical and horizontal axis are the log-fold-change-ratios on a log-equivalent transformed scale, denoted M = glog(S/Q), and the log-geometric-means on a log-equivalent transformed scale, denoted A = ½*glog(S*Q) respectively. Solid lines in the MA plot represent the LOESS smoothing curves of the differentially expressed genes (red and green) and non-regulated genes (blue).