The Construction of Genome-Based Transcriptional Units Export

@article{citeulike:4235916, abstract = {Abstract 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.}, author = {van Hooff, Sander R. and Koster, Jan and Hulsen, Tim and van Schaik, Barbera D. C. and Roos, Marco and van Batenburg, Marcel F. and Versteeg, Rogier and van Kampen, Antoine H. C.}, citeulike-article-id = {4235916}, citeulike-linkout-0 = {http://dx.doi.org/10.1089/omi.2008.0036}, citeulike-linkout-1 = {http://www.liebertonline.com/doi/abs/10.1089/omi.2008.0036}, doi = {10.1089/omi.2008.0036}, journal = {OMICS: A Journal of Integrative Biology}, keywords = {alternative-splicing}, number = {0}, pages = {1--10}, posted-at = {2009-03-30 05:38:12}, priority = {2}, title = {The Construction of Genome-Based Transcriptional Units}, url = {http://dx.doi.org/10.1089/omi.2008.0036}, volume = {0}, year = {0} }

TY - JOUR ID - citeulike:4235916 L3 - citeulike-article-id:4235916 N2 - Abstract 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. IS - 0 JF - OMICS: A Journal of Integrative Biology EP - 10 TI - The Construction of Genome-Based Transcriptional Units VL - 0 SP - 1 KW - alternative-splicing AU - van Hooff, Sander AU - Koster, Jan AU - Hulsen, Tim AU - van Schaik, Barbera AU - Roos, Marco AU - van Batenburg, Marcel AU - Versteeg, Rogier AU - van Kampen, Antoine PY - 2000/// UR - http://dx.doi.org/10.1089/omi.2008.0036 ER -