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

BioData Mining

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

[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

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

Others  :  797343
DOI  :  10.1186/1756-0381-4-15

 received in 2011-03-08, accepted in 2011-06-14,  发布年份 2011

【 摘 要 】

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.

【 授权许可】

   
2011 Echeverría et al; licensee BioMed Central Ltd.

【 图 表 】

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