Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs

作者：Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin C. Frith, Pär G. Engström, Boris Lenhard, Rajith N. Aturaliya, Serge Batalov, Kirk W. Beisel, Carol J. Bult, Colin Fletcher, Alistair R. R. Forrest, Masaaki Furuno, David P. Hill, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Shintaro Katayama, Masaru Katoh, Tsugumi Kawashima, John Quackenbush, Timothy Ravasi, Brian Z. Ring, Kazuhiro Shibata, Koji Sugiura, Yoichi Takenaka, Rohan David Teasdale, Christine Anne Wells, Yunxia Zhu, Chikatoshi Kai, Jun Kawai, David Hume, Piero Carninci, Yoshihide Hayashizaki · 发表于：PLoS Genetics · 年份：2006 · DOI：10.1371/journal.pgen.0020062 · 被引用次数：186 · 研究领域：Genomics and Phylogenetic Studies、Advanced Proteomics Techniques and Applications、Identification and Quantification in Food

The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full-length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web-based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full-length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding (including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full-length cDNAs. The total number of di...