Measuring similarities between transcription factor binding sites

BMC Bioinformatics. 2005 Sep 28;6:237. doi: 10.1186/1471-2105-6-237.


Background: Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites.

Results: We propose to identify and group similar profiles using two independent similarity measures: chi2 distances between position frequency matrices (PFMs) and correlation coefficients between position weight matrices (PWMs) scores.

Conclusion: We show that these measures complement each other and allow to associate Jaspar and Transfac matrices. Clusters of highly similar matrices are identified and can be used to optimise the search for regulatory elements. Moreover, the application of the measures is illustrated by assigning E-box matrices of a SELEX experiment and of experimentally characterised binding sites of circadian clock genes to the Myc-Max cluster.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ARNTL Transcription Factors
  • Basic Helix-Loop-Helix Transcription Factors / metabolism
  • Binding Sites
  • Chromosome Mapping / methods*
  • Circadian Rhythm / genetics
  • Databases, Nucleic Acid
  • E-Box Elements / physiology
  • Models, Biological*
  • Nucleotides / analysis
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / methods
  • Transcription Factors / metabolism*


  • ARNTL Transcription Factors
  • Basic Helix-Loop-Helix Transcription Factors
  • Nucleotides
  • Transcription Factors