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Related Experiment Videos

Assessment of SAGE in transcript identification.

Erin D Pleasance1, Marco A Marra, Steven J M Jones

  • 1Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver V5Z 4E6, Canada.

Genome Research
|May 14, 2003
PubMed
Summary

This study introduces a new method for mapping Serial Analysis of Gene Expression (SAGE) tags, improving transcript identification in model organisms. The approach reveals limitations in current SAGE procedures for detecting gene expression.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Serial Analysis of Gene Expression (SAGE) is crucial for transcript profiling.
  • Current SAGE tag mapping resources are incomplete, limiting assessment of SAGE efficacy.
  • Unambiguous gene identification from SAGE tags remains a challenge.

Purpose of the Study:

  • To develop and apply a novel method for SAGE tag mapping.
  • To provide comprehensive tag-to-gene mapping resources for *Drosophila melanogaster* and *Caenorhabditis elegans*.
  • To assess the limitations of standard SAGE for transcript identification.

Main Methods:

  • Constructed a conceptual transcriptome using genomic data, EST/cDNA alignments, UTR information, and polyadenylation signals.
  • Applied the method to *D. melanogaster* and *C. elegans* genomes.

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  • Analyzed SAGE tag data to identify genes with ambiguous or undetectable expression.

    • Main Results:

    • Developed a new tag-mapping method and created valuable resources for *D. melanogaster* and *C. elegans*.
    • Identified that standard SAGE cannot unambiguously detect 8% of *D. melanogaster* and 15% of *C. elegans* genes.
    • Found that increasing tag length or altering the anchoring enzyme (e.g., using Sau3A instead of NlaIII) can enhance transcript detection.

    Conclusions:

    • The developed method enables detailed SAGE assessment and provides essential tag-mapping data.
    • Quantified genes not amenable to standard SAGE analysis due to technical limitations.
    • Suggests modifications to SAGE protocols to improve transcript detection efficiency.