Transcript annotation in FANTOM 3

T he 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 themouse proteome by full-length cDNAs. The total number of distinct non-protein-coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and final expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species. Citation: Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, et al. (2006) Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs. PLoS Genet 2(4): e62. DOI: 10.1371/journal.pgen. 0020062 DOI: 10.1371/journal.pgen. 0020062 Copyright: 2006 Maeda et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abbreviations: CDS, coding sequence; GO, Gene Ontology; MGI, Mouse Genome Informatics; ncRNA, noncoding RNA N. Maeda, M. Itoh, K. Shibata, J. Kawai, P. Carninci, and Y. Hayashizaki are in the Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan. T. Kasukawa, R. Oyama, J. Gough, M. Frith, M. Kanamori-Katayama, S. Katayama, T. Kawashima, C. Kai, J. Kawai, P. Carninci, and Y. Hayashizaki are in the Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan. T. Kasukawa is in the Broadband Communication Service Business Unit, Network Service Solution Business Group, NTT Software Corporation, Yokohama, Japan. M. Frith, R. N. Aturaliya, and R. D. Teasdale are at the Australian Research Council Center in Bioinformatics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia. P. G. Engström and B. Lenhard are in the Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway, and the Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden. S. Batalov and C. F. Fletcher are at the Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America. K. W. Beisel is in the Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska, United States of America. C. J. Bult, M. Furuno, D. Hill, and Y. Zhu are in the Mouse Genome Informatics Consortium, The Jackson Laboratory, Bar Harbor, Maine, United States of America. A. R. R. Forrest, T. Ravasi, and D. A. Hume are at the Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia. M. Katoh is in the Genetics and Cell Biology Section, National Cancer Center Research Institute, Tokyo, Japan. J. Quackenbush is at the Institute for Genomic Research, Rockville, Maryland, United States of America. B. Z. Ring is at Applied Genomics, Sunnyvale, California, United States of America. K. Sugiura is at The Jackson Laboratory, Bar Harbor, Maine, United States of America. Y. Takenaka is in the Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan. C. A. Wells is in the School of Biomolecular and Biomedical Science, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan, Queensland, Australia. Y. Hayashizaki is at Yokohama City University, Yokohama, Japan, and in the Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan. * To whom correspondence should be addressed. E-mail: rgscerg@gsc.riken. jp ¤a Current address: Functional Genomics Subunit, Center for Developmental Biology, RIKEN, Kobe, Japan ¤b Current address: Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, United States of America PLoS Genetics | www.plosgenetics. org April 2006 | Volume 2 | Issue 4 | e62 0498