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Related Experiment Videos

AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.

Vincent Le Texier1, Jean-Jack Riethoven, Vasudev Kumanduri

  • 1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. texier@ebi.ac.uk

BMC Bioinformatics
|March 25, 2006
PubMed
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This study integrates data on alternative splicing and polyadenylation to identify transcript variants. Alternative splicing plays a larger role in transcript diversity than alternative polyadenylation.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transcript formation is regulated by transcription start (TS) selection, splicing, and polyadenylation.
  • Current data collection and annotation for these transcript variants are often individualized.
  • An integrated view of these datasets is crucial for understanding transcript diversity.

Purpose of the Study:

  • To extend existing computational pipelines (AltSplice, AltPAS) for a comprehensive analysis of transcript variants.
  • To integrate data on alternative splicing and polyadenylation for a unified view of transcript formation.
  • To create a consolidated dataset and web resource for alternate transcript diversity.

Main Methods:

  • The AltTrans pipeline was developed, extending AltSplice, to delineate isoform transcript patterns including splicing and polyadenylation sites.

Related Experiment Videos

  • The AltPAS pipeline identifies all potential polyadenylation sites.
  • Data from AltTrans and AltPAS were merged, and the integrated dataset was annotated for biological features.

    • Main Results:

    • A comprehensive dataset on alternative splicing, alternative polyadenylation, and resultant transcript patterns was generated for human and mouse.
    • The integrated data is accessible via the Alternate Transcript Diversity website.
    • Analysis of current transcriptome data reveals the significant contribution of alternative splicing to transcript diversity.

    Conclusions:

    • The study presents an annotated dataset of alternate transcript patterns, incorporating both alternative splicing and polyadenylation.
    • Findings indicate that alternative splicing is a more dominant mechanism in generating transcript diversity compared to alternative polyadenylation.