Figure 2

Visualization of the pairwise comparisons of the microarray data by a dynamic graph. Genes showing significant fold change in their expression levels in at least one pairwise comparison of all the experimental conditions were linked and grouped according to their coexpression levels along the experiments, their interactions at the protein levels (relatively few in this particular dataset) and their cellular localization. (A) Nodes represent genes (and gene products). These nodes are colored with a red-to-green gradient according to their expression/fold change values, where red and green represent up-regulation and down-regulation, respectively (see inset for color gradient). For dynamic visualization, these graphs were converted into an animation. (B) The TF enrichment analysis of genes that are up-regulated upon Hsp90 inhibition showed that most of the red nodes correspond to genes that are potentially regulated by STREs (highlighted red nodes). (C) The repeated observation of the dynamic graph (animation), allows the identification of groups of nodes sharing the same color patterns because of their particular expression levels across all experiments. The regions highlighted with pastel colors indicate the positions in the graph where a majority of the nodes defining each pattern were identified.