Negative information for motif discovery

  • Takusagawa K
  • Gifford D
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We discuss a method of combining genome-wide transcription
factor binding data, gene expression data, and genome
sequence data for the purpose of motif discovery in S.
cerevisiae. Within the word-counting algorithmic approach to
motif discovery, we present a method of incorporating
information from negative intergenic regions where a
transcription factor is thought not to bind, and a
statistical significance measure which account for
intergenic regions of different lengths. Our results
demonstrate that our method performs slightly better than
other motif discovery algorithms. Finally, we present
significant potential new motifs discovered by the

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  • PMID: 14992517


  • K T Takusagawa

  • D K Gifford

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