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  • A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE

    Author(s)
    J. Faulkner, Geoffrey
    Forrest, Alistair
    Chalk, Alistair
    Schroder, Kate
    Hayashizaki, Yoshihide
    Carninci, Piero
    A. Hume, David
    M. Grimmond, Sean
    Griffith University Author(s)
    Chalk, Alistair M.
    Forrest, Alistair RR.
    Year published
    2008
    Metadata
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    Abstract
    Cap analysis gene expression (CAGE) is a high-throughput, tag-based method designed to survey the 5' end of capped full-length cDNAs. CAGE has previously been used to define global transcription start site usage and monitor gene activity in mammals. A drawback of the CAGE approach thus far has been the removal of as many as 40% of CAGE sequence tags due to their mapping to multiple genomic locations. Here, we address the origins of multimap tags and present a novel strategy to assign CAGE tags to their most likely source promoter region. When this approach was applied to the FANTOM3 CAGE libraries, the percentage of ...
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    Cap analysis gene expression (CAGE) is a high-throughput, tag-based method designed to survey the 5' end of capped full-length cDNAs. CAGE has previously been used to define global transcription start site usage and monitor gene activity in mammals. A drawback of the CAGE approach thus far has been the removal of as many as 40% of CAGE sequence tags due to their mapping to multiple genomic locations. Here, we address the origins of multimap tags and present a novel strategy to assign CAGE tags to their most likely source promoter region. When this approach was applied to the FANTOM3 CAGE libraries, the percentage of protein-coding mouse transcriptional frameworks detected by CAGE improved from 42.9 to 57.8% (an increase of 5516 frameworks) with no reduction in CAGE to microarray correlation. These results suggest that the multimap tags produced by high-throughput, short sequence tag-based approaches can be rescued to augment greatly the transcriptome coverage provided by single-map tags alone.
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    Journal Title
    Genomics
    Volume
    91
    Issue
    3
    DOI
    https://doi.org/10.1016/j.ygeno.2007.11.003
    Subject
    Genetics
    Information Systems
    Publication URI
    http://hdl.handle.net/10072/20261
    Collection
    • Journal articles

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