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Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.

Maeda, Norihiro and Kasukawa, Takeya and Oyama, Rieko and Gough, Julian and Frith, Martin and Engström, Pär G and Lenhard, Boris and Aturaliya, Rajith N and Batalov, Sergei and Beisel, Kirk W and Bult, Carol J and Fletcher, Colin and Forrest, Alistair R R and Furuno, Masaaki and Hill, David and Itoh, Masayoshi and Kanamori-Katayama, Mutsumi and Katayama, Shintaro and Katoh, Masaru and Kawashima, Tsugumi and Quackenbush, John and Ravasi, Timothy and Ring, Brian Z and Shibata, Kazuhiro and Sugiura, Koji and Takenaka, Yoichi and Teasdale, Rohan D and Wells, Christine A and Zhu, Yunxia and Kai, Chikatoshi and Kawai, Jun and Hume, David A and Carninci, Piero and Hayashizaki, Yoshihide (2006) Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genetics, 2 (4). e62. ISSN 1553-7404

Abstract

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 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.

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Date Deposited: 13 Oct 2015 13:17
Last Modified: 13 Oct 2015 13:17
URI: https://oak.novartis.com/id/eprint/93

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