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Open Access Research

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

Pablo C Echeverría1, Fedor Forafonov1, Deo P Pandey2, Guillaume Mühlebach1 and Didier Picard1*

Author Affiliations

1 Département de Biologie Cellulaire, Université de Genève, Sciences 3, CH - 1211 Genève 4, Switzerland

2 Biotech Research and Innovation Center (BRIC), University of Copenhagen, Ole Maaloes vej 5, 2200 Copenhagen, Denmark

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BioData Mining 2011, 4:15  doi:10.1186/1756-0381-4-15

Published: 14 June 2011

Abstract

Background

To make sense out of gene expression profiles, such analyses must be pushed beyond the mere listing of affected genes. For example, if a group of genes persistently display similar changes in expression levels under particular experimental conditions, and the proteins encoded by these genes interact and function in the same cellular compartments, this could be taken as very strong indicators for co-regulated protein complexes. One of the key requirements is having appropriate tools to detect such regulatory patterns.

Results

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.

Conclusions

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.

Keywords:
gene expression; microarray analysis; visualization; yeast; stress response; molecular chaperones; Hsp90; inhibitor; gene deletion