title: Saccharomyces cerevisiae as a model organism: a comparative study.
abstract: BACKGROUND
  Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. Such organisms should be representative of the living beings for which they are to serve as proxy. However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking.
  
  
  RESULTS
  In this work we propose such a method and apply it in a pilot study of strengths and limitations of Saccharomyces cerevisiae as a model organism. The method relies on the functional classification of proteins into different biological pathways and processes and on full proteome comparisons between the putative model organism and other organisms for which we would like to extrapolate results. Here we compare S. cerevisiae to 704 other organisms from various phyla. For each organism, our results identify the pathways and processes for which S. cerevisiae is predicted to be a good model to extrapolate from. We find that animals in general and Homo sapiens in particular are some of the non-fungal organisms for which S. cerevisiae is likely to be a good model in which to study a significant fraction of common biological processes. We validate our approach by correctly predicting which organisms are phenotypically more distant from S. cerevisiae with respect to several different biological processes.
  
  
  CONCLUSIONS
  The method we propose could be used to choose appropriate substitute model organisms for the study of biological processes in other species that are harder to study. For example, one could identify appropriate models to study either pathologies in humans or specific biological processes in species with a long development time, such as plants.
authors.affiliation: Departament Ciències Mèdiques Bàsiques, Universitat de Lleida & IRBLleida, Lleida, Spain.
authors.forename: Hiren
authors.initials: H
authors.lastname: Karathia
authors.forename: Ester
authors.initials: E
authors.lastname: Vilaprinyo
authors.forename: Albert
authors.initials: A
authors.lastname: Sorribas
authors.forename: Rui
authors.initials: R
authors.lastname: Alves
mesh_terms: D000818:Animals; D001105:Archaea / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D056890:Eukaryota / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D005544:Forecasting; D053858:Metabolic Networks and Pathways / Q000235:genetics / Q000502:physiology; D008962:Models, Theoretical; D010802:Phylogeny; D010865:Pilot Projects; D012107:Research Design; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics; D054928:Validation Studies as Topic