Revealing modular organization in the yeast transcriptional network

Nat Genet. 2002 Aug;31(4):370-7. doi: 10.1038/ng941. Epub 2002 Jul 22.


Standard clustering methods can classify genes successfully when applied to relatively small data sets, but have limited use in the analysis of large-scale expression data, mainly owing to their assignment of a gene to a single cluster. Here we propose an alternative method for the global analysis of genome-wide expression data. Our approach assigns genes to context-dependent and potentially overlapping 'transcription modules', thus overcoming the main limitations of traditional clustering methods. We use our method to elucidate regulatory properties of cellular pathways and to characterize cis-regulatory elements. By applying our algorithm systematically to all of the available expression data on Saccharomyces cerevisiae, we identify a comprehensive set of overlapping transcriptional modules. Our results provide functional predictions for numerous genes, identify relations between modules and present a global view on the transcriptional network.

Publication types

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

MeSH terms

  • Algorithms*
  • Citric Acid Cycle
  • Gene Expression Regulation, Fungal*
  • Models, Genetic
  • Regulatory Sequences, Nucleic Acid
  • Reproducibility of Results
  • Transcription, Genetic*
  • Yeasts / genetics*
  • Yeasts / metabolism