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Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements

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Systems Biology and Regulatory Genomics (RSB 2005, RRG 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4023))

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Abstract

It has been a challenge to discover transcription factor (TF) binding motifs (TFBMs), which are short cis-regulatory DNA sequences playing essential roles in transcriptional regulation. We approach the problem of discovering TFBMs from a steganographic perspective. We view the regulatory regions of a genome as if they constituted a stegoscript with conserved words (i.e., TFBMs) being embedded in a covertext, and model the stegoscript with a statistical model consisting of a dictionary and a grammar. We develop an efficient algorithm, WordSpy, to learn such a model from a stegoscript and to recover conserved motifs. Subsequently, we select biologically meaningful motifs based on a motif’s specificity to the set of genes of interest and/or the expression coherence of the genes whose promoters contain the motif. From the promoters of 645 distinct cell-cycle related genes of S. cerevisiae, our method is able to identify all known cell-cycle related TFBMs among its top ranking motifs. Our method can also be directly applied to discriminative motif finding. By utilizing the ChIP-chip data of Lee et al., we predicted potential binding motifs of 113 known transcription factors of budding yeast.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering,  

    Guandong Wang & Weixiong Zhang

  2. Department of Genetics, Washington University in Saint Louis, Saint Louis, MO 63130-4899, USA

    Weixiong Zhang

Authors
  1. Guandong Wang
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  2. Weixiong Zhang
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Eleazar Eskin Trey Ideker Ben Raphael Christopher Workman

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© 2007 Springer Berlin Heidelberg

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Wang, G., Zhang, W. (2007). Build a Dictionary, Learn a Grammar, Decipher Stegoscripts, and Discover Genomic Regulatory Elements. In: Eskin, E., Ideker, T., Raphael, B., Workman, C. (eds) Systems Biology and Regulatory Genomics. RSB RRG 2005 2005. Lecture Notes in Computer Science(), vol 4023. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-48540-7_8

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  • DOI: https://doi.org/10.1007/978-3-540-48540-7_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-48293-2

  • Online ISBN: 978-3-540-48540-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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