Yeast genomic expression studies using DNA microarrays

Methods Enzymol. 2002;350:393-414. doi: 10.1016/s0076-6879(02)50976-9.


The exploration and characterization of yeast genomic expression programs is providing a wealth of information about yeast biology, as well as other organisms. The intriguing biology of yeast species invites characterization of genomic expression patterns to illuminate the details of cellular physiology. In addition to its value as an interesting organism, yeast maintains its role as an excellent model in which to characterize genomic expression programs. Microarray studies are quickly spreading to plant, animal, and microbial organisms that remain in the early stages of characterization. The extensive knowledge of yeast biology, as well as the relative ease with which yeast studies can be performed and controlled, facilitates interpretation of the genomic expression data. Importantly, existing information about yeast biology, including functional annotations for each gene, is captured and efficiently presented in databases such as the Saccharomyces Genome Database (SGD), the Munich Information Center Yeast Genome Database (MIPS), the Yeast and Pombe Protein Databases (YPD and PPD, respectively), and others. A number of databases also allow the exploration of published genomic expression studies, including the "Expression Connection" at SGD and the Microarray Global Viewer (yMGV) organized by Marc et al. Consulting these databases to retrieve known details about gene function and regulation vastly facilitates interpretation of the genomic expression data, allowing biological hypotheses to be formulated and tested. These hypotheses can be applied to other organisms that may execute genomic expression programs similar to those seen in yeast. Furthermore, as more genomic expression studies in multiple organisms emerge, large-scale data comparisons can be conducted, within and across organisms. Incorporating the results of yeast studies into such comparisons is certain to increase our understanding about the function, regulation, and evolution of genomic expression programs.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Carbocyanines
  • Deoxyuracil Nucleotides
  • Fluorescent Dyes
  • Gene Expression Profiling / methods*
  • Genome, Fungal*
  • Oligonucleotide Array Sequence Analysis / methods*
  • RNA / isolation & purification
  • Staining and Labeling / methods
  • Transcription, Genetic
  • Yeasts / genetics*


  • 3'-deoxy-5-(cyanine dye 3)uridine 5'-trisphosphate
  • 3'-deoxy-5-(cyanine dye 5)uridine 5'-trisphosphate
  • Carbocyanines
  • Deoxyuracil Nucleotides
  • Fluorescent Dyes
  • RNA