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Computational Prediction of Genes Translationally Regulated by Cytoplasmic Polyadenylation Elements

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Bioinformatics and Computational Biology (BICoB 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5462))

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Abstract

Cytoplasmic post-transcriptional modification of mRNA transcripts in the form of polyadenylated (poly(A)) tails plays a key role in their translational control. The timing and degree of polyadenylation has been shown to be due in part to a consensus nucleotide sequence – cytoplasmic polyadenylation elements (CPEs) which can be detected by a polyadenylation element binding protein (CPEB). An individual mRNA transcript controlled by CPEB may contain one or more CPE sites occurring upstream of a consensus hexamer poly-(A) signal. A probabilistic model, CPEDetector, is presented for predicting whether or not a gene’s translation is mediated by CPEB. CPEDetector takes into account detected CPE sites, poly-A sites, and distance metrics between the detected locations. This approach is tested against the 3’ untranslated regions (UTRs) of known genes using the UTRdb database.

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Author information

Authors and Affiliations

  1. Department of Computer Engineering and Computer Science, J.B. Speed School of Engineering, University of Louisville, 123 JB Speed Building, Louisville, Kentucky, USA

    Eric C. Rouchka

  2. Department of Anatomical Sciences and Neurobiology, University of Louisville, 500 South Preston Street, Louisville, Kentucky, USA

    Xiangping Wang & Nigel G. F. Cooper

  3. Department of Electrical and Computer Engineering, J.B. Speed School of Engineering, University of Louisville, Louisville, Kentucky, USA

    James H. Graham

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  1. Eric C. Rouchka
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  2. Xiangping Wang
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  3. James H. Graham
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  4. Nigel G. F. Cooper
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Editors and Affiliations

  1. Department of Computer Science and Engineering, University of Connecticut, 257 ITE Building, 371 Fairfield Way, CT 06269-2155, Storrs, USA

    Sanguthevar Rajasekaran

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© 2009 Springer-Verlag Berlin Heidelberg

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Rouchka, E.C., Wang, X., Graham, J.H., Cooper, N.G.F. (2009). Computational Prediction of Genes Translationally Regulated by Cytoplasmic Polyadenylation Elements. In: Rajasekaran, S. (eds) Bioinformatics and Computational Biology. BICoB 2009. Lecture Notes in Computer Science(), vol 5462. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00727-9_33

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  • DOI: https://doi.org/10.1007/978-3-642-00727-9_33

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-00726-2

  • Online ISBN: 978-3-642-00727-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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