Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation

We have analyzed the global adaptations in gene expression patterns in the budding yeast when the Hsp90 molecular chaperone complex is perturbed either pharmacologically or genetically. We integrated these results with publicly accessible expression, protein-protein interaction and intracellular localization data. But most importantly, all experimental conditions were simultaneously and dynamically visualized with an animation. This critically facilitated the detection of patterns of gene expression changes that suggested underlying regulatory networks that a standard analysis by pairwise comparison and clustering could not have revealed.The results of the animation-assisted detection of changes in gene regulatory patterns make predictions about the potential roles of Hsp90 and its co-chaperone p23 in regulating whole sets of genes. The simultaneous dynamic visualization of microarray experiments, represented in networks built by integrating one's own experimental with publicly accessible data, represents a powerful discovery tool that allows the generation of new interpretations and hypotheses.In the current post-genomic era, an increasing amount of data is generated by the application of high-throughput technologies. Expression profiling analyses using DNA microarray approaches are extensively used to study global changes in gene expression patterns of multiple cell types and tissues under different conditions. Moreover, there are publicly accessible databases containing the experimentally established DNA binding sequences for transcription factors (TF). To identify interaction partners of a protein of interest, several large-scale methods such as yeast two-hybrid screens, tandem affinity purification followed by mass spectrometric analyses, and protein chips are commonly used. Proteome-wide studies to identify protein-protein interaction (PPI) partners for many proteins have resulted in several publicly available and well-curated databases, which can be used to e