Figure 2.

The four major expression patterns in the damage-induced gene set revealed by cluster analysis. For each of the 112 damage-induced genes, the fold change in expression level 4 h after NCS treatment was computed in uninfected cells and in the cells knocked-down for Rel-A, p53 and ATM, yielding a 112 × 4 data matrix, with the rows corresponding to genes. This matrix was subjected to hierarchical clustering after normalizing the rows to have mean = 0 and SD = 1. The heat map visually represents the normalized matrix after being clustered. Red, green and black entries represent above-, below- and near-average fold change of induction, respectively. Four prominent expression patterns are evident. Cluster 1 represents genes whose induction is strongly attenuated in cells knocked-down for Rel-A and ATM (compared to the response in the control uninfected cells), and only partially attenuated in cells knocked-down for p53. Cluster 2 represents genes whose response is attenuated in cells knocked-down for p53 and ATM, but augmented in cells knocked-down for Rel-A. Cluster 3 represents genes whose response is attenuated in cells knocked-down for p53 and ATM, but not affected by knocking-down Rel-A. Cluster 4 represents genes whose response is markedly attenuated in cells knocked-down for p53, and only partially attenuated in cells knocked-down for ATM.