Kasukawa Takeya, Katayama Shintaro, Kawaji Hideya, Suzuki Harukazu, Hume David A, Hayashizaki Yoshihide
Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045, Japan.
Genomics. 2004 Dec;84(6):913-21. doi: 10.1016/j.ygeno.2004.08.011.
The number of mammalian transcripts identified by full-length cDNA projects and genome sequencing projects is increasing remarkably. Clustering them into a strictly nonredundant and comprehensive set provides a platform for functional analysis of the transcriptome and proteome, but the quality of the clustering and predictive usefulness have previously required manual curation to identify truncated transcripts and inappropriate clustering of closely related sequences. A Representative Transcript and Protein Sets (RTPS) pipeline was previously designed to identify the nonredundant and comprehensive set of mouse transcripts based on clustering of a large mouse full-length cDNA set (FANTOM2). Here we propose an alternative method that is more robust, requires less manual curation, and is applicable to other organisms in addition to mouse. RTPSs of human, mouse, and rat have been produced by this method and used for validation. Their comprehensiveness and quality are discussed by comparison with other clustering approaches. The RTPSs are available at .
通过全长cDNA项目和基因组测序项目鉴定出的哺乳动物转录本数量正在显著增加。将它们聚类成一个严格非冗余且全面的集合，为转录组和蛋白质组的功能分析提供了一个平台，但聚类的质量和预测实用性此前需要人工整理，以识别截短的转录本和密切相关序列的不恰当聚类。此前设计了一种代表性转录本和蛋白质集（RTPS）流程，基于对大量小鼠全长cDNA集（FANTOM2）的聚类来鉴定小鼠转录本的非冗余且全面的集合。在此，我们提出一种更稳健、所需人工整理更少且除小鼠外还适用于其他生物的替代方法。通过此方法已生成了人、小鼠和大鼠的RTPS并用于验证。通过与其他聚类方法比较，讨论了它们的全面性和质量。RTPS可在……获取。
