title: Colony size measurement of the yeast gene deletion strains for functional genomics.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada. nmemarian@comm.utoronto.ca <nmemarian@comm.utoronto.ca>
authors.forename: Negar
authors.initials: N
authors.lastname: Memarian
authors.forename: Matthew
authors.initials: M
authors.lastname: Jessulat
authors.forename: Javad
authors.initials: J
authors.lastname: Alirezaie
authors.forename: Nadereh
authors.initials: N
authors.lastname: Mir-Rashed
authors.forename: Jianhua
authors.initials: J
authors.lastname: Xu
authors.forename: Mehri
authors.initials: M
authors.lastname: Zareie
authors.forename: Myron
authors.initials: M
authors.lastname: Smith
authors.forename: Ashkan
authors.initials: A
authors.lastname: Golshani
mesh_terms: D000465:Algorithms; D018797:Cell Cycle Proteins / Q000235:genetics*; D049109:Cell Proliferation; D002874:Chromosome Mapping / Q000379:methods*; D015169:Colony Count, Microbial / Q000379:methods*; D003198:Computer Simulation; D004260:DNA Repair / Q000502:physiology*; D017353:Gene Deletion; D023281:Genomics / Q000379:methods*; D048369:MAP Kinase Kinase 1 / Q000235:genetics*; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000502:physiology*; D029702:Schizosaccharomyces pombe Proteins / Q000235:genetics*; D012984:Software; D013045:Species Specificity
chemical_list: D018797:Cell Cycle Proteins; D029701:Saccharomyces cerevisiae Proteins; D029702:Schizosaccharomyces pombe Proteins; C119549:Mek1 protein, S pombe; D048369:MAP Kinase Kinase 1