Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms

Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3351-6. doi: 10.1073/pnas.0530258100. Epub 2003 Mar 11.


We describe a comparative mathematical framework for two genome-scale expression data sets. This framework formulates expression as superposition of the effects of regulatory programs, biological processes, and experimental artifacts common to both data sets, as well as those that are exclusive to one data set or the other, by using generalized singular value decomposition. This framework enables comparative reconstruction and classification of the genes and arrays of both data sets. We illustrate this framework with a comparison of yeast and human cell-cycle expression data sets.

Publication types

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

MeSH terms

  • Cell Cycle / genetics
  • Data Interpretation, Statistical
  • Databases, Genetic
  • Gene Expression Profiling / statistics & numerical data*
  • Genes, Fungal / drug effects
  • Genomics / statistics & numerical data*
  • Humans
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Pheromones / pharmacology
  • RNA, Fungal / genetics
  • RNA, Fungal / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Saccharomyces cerevisiae / cytology
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Stress, Physiological / genetics


  • Pheromones
  • RNA, Fungal
  • RNA, Messenger