The construction of genome-based transcriptional units

Sander R. Van Hooff, Jan Koster, Tim Hulsen, Barbera D.C. Van Schaik, Marco Roos, Marcel F. Van Batenburg, Rogier Versteeg, Antoine H.C. Van Kampen

Onderzoeksoutput: Bijdrage aan tijdschriftArtikelpeer review


Gene-oriented sequence clusters (transcriptional units) have found many applications in genomics research including the construction of transcriptome maps and identification of splice variants. We developed a new method to construct transcriptional that uses the genomic sequence as a template. We present and discuss our method in detail together with an evaluation of the transcriptional units for human. We constructed 33,007 and 27,792 transcriptional units for human and mouse, respectively. The sensitivity (81) and specificity (90) of our method compares favorably to other established methods. We evaluated the representation of experimentally validated and predicted intergenic spliced transcripts in humans and show that we correctly represent a large fraction of these cases by single transcriptional units. Our method performs well, but the evaluation of the final set of transcriptional units show that improvements to the algorithm are still possible. However, because the precise number and types of errors are difficult to track, it is not obvious how to significantly improve the algorithm. We believe that ongoing research efforts are necessary to further improve current methods. This should include detailed documentation, comparison, and evaluation of current methods.

Originele taal-2Engels
Pagina's (van-tot)105-114
Aantal pagina's10
TijdschriftOMICS A Journal of Integrative Biology
Nummer van het tijdschrift2
StatusGepubliceerd - 1 apr. 2009
Extern gepubliceerdJa


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