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Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data

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  • Siewert Elizabeth A

    (University of Colorado, Denver)

  • Kechris Katerina J

    (University of Colorado, Denver)

Abstract

De novo identification of transcription factor binding sites (TFBS) is a challenging computational problem because TFBSs are relatively short sequences buried in long genomic regions. Earlier methods incorporated genome-wide expression data and promoter sequences into a linear-model framework, regressing expression on counts of putative TFBSs in promoters for a single species. More recently, it has been shown that examining sequence data across multiple species improves the prediction of TFBSs. In this work, we describe an extension of the single-species, linear-model framework for the analysis of paired cross-species sequence and expression data. A repeated measures model for gene-expression measurements across species is used, accounting for phylogenetic relationships among species through the error covariance structure. This multiple-species algorithm is applied to a data set of four yeast species grown under heat-shock conditions and comparisons are made to the single species algorithm. Using evaluations based on transcription factor binding strength and an independent source of expression data, we find the multiple species results show an improvement in the prediction of TFBS.

Suggested Citation

  • Siewert Elizabeth A & Kechris Katerina J, 2009. "Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-36, September.
    • Handle: RePEc:bpj:sagmbi:v:8:y:2009:i:1:n:36
    DOI: 10.2202/1544-6115.1464
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    References listed on IDEAS

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    1. Rahul Siddharthan & Eric D Siggia & Erik van Nimwegen, 2005. "PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny," PLOS Computational Biology, Public Library of Science, vol. 1(7), pages 1-23, December.
    2. Sunduz Keles & Mark van der Laan & Chris Vulpe, 2004. "Regulatory Motif Finding by Logic Regression," U.C. Berkeley Division of Biostatistics Working Paper Series 1145, Berkeley Electronic Press.
    3. Scott A. Rifkin & David Houle & Junhyong Kim & Kevin P. White, 2005. "A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression," Nature, Nature, vol. 438(7065), pages 220-223, November.
    4. Manolis Kellis & Nick Patterson & Matthew Endrizzi & Bruce Birren & Eric S. Lander, 2003. "Sequencing and comparison of yeast species to identify genes and regulatory elements," Nature, Nature, vol. 423(6937), pages 241-254, May.
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    1. Tuglus Catherine & van der Laan Mark J., 2011. "Repeated Measures Semiparametric Regression Using Targeted Maximum Likelihood Methodology with Application to Transcription Factor Activity Discovery," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-31, January.

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