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Open Access Research article

Colony size measurement of the yeast gene deletion strains for functional genomics

Negar Memarian12, Matthew Jessulat3, Javad Alirezaie24, Nadereh Mir-Rashed3, Jianhua Xu5, Mehri Zareie6, Myron Smith3 and Ashkan Golshani37*

Author Affiliations

1 Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada

2 Department of Electrical Engineering, Ryerson University, Toronto, Canada

3 Department of Biology, Carleton University, Ottawa, Canada

4 Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada

5 The Best Institute, University of Toronto, Toronto, Canada

6 Department of Molecular and Medical Genetics, University of Toronto, Toronto, Canada

7 Ottawa Institute of System Biology, Ottawa, Canada

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BMC Bioinformatics 2007, 8:117  doi:10.1186/1471-2105-8-117

Published: 4 April 2007

Abstract

Background

Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences.

Results

Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research.

Conclusion

GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations.