Regulatory element detection using correlation with expression

Nat Genet. 2001 Feb;27(2):167-71. doi: 10.1038/84792.


We present here a new computational method for discovering cis-regulatory elements that circumvents the need to cluster genes based on their expression profiles. Based on a model in which upstream motifs contribute additively to the log-expression level of a gene, this method requires a single genome-wide set of expression ratios and the upstream sequence for each gene, and outputs statistically significant motifs. Analysis of publicly available expression data for Saccharomyces cerevisiae reveals several new putative regulatory elements, some of which plausibly control the early, transient induction of genes during sporulation. Known motifs generally have high statistical significance.

Publication types

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

MeSH terms

  • Algorithms*
  • Binding Sites
  • Cell Cycle / genetics
  • Consensus Sequence
  • DNA-Binding Proteins / metabolism
  • Gene Expression Regulation, Fungal*
  • Minichromosome Maintenance 1 Protein
  • Models, Theoretical*
  • Regulatory Sequences, Nucleic Acid*
  • Saccharomyces cerevisiae / cytology
  • Saccharomyces cerevisiae / genetics*
  • Transcription Factors / metabolism


  • DNA-Binding Proteins
  • Minichromosome Maintenance 1 Protein
  • Transcription Factors