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

    Author(s)
    Maeda, Norihiro
    Kasukawa, Takeya
    Oyama, Rieko
    Gough, Julian
    Frith, Martin
    Engstrom, Par
    Lenhard, Boris
    Aturaliya, Rajith
    Batalov, Serge
    Beisel, Kirk W
    Bult, Carol J
    Fletcher, Colin F
    Forrest, Alistair Raymond Russell
    Furuno, Masaaki
    Hill, David
    Itoh, Masayoshi
    Kanamori-Katayama, Mutsumi
    Katayama, Shintaro
    Katoh, Masaru
    Kawashima, Tsugumi
    Quackenbush, John
    Ravasi, Timothy
    Ring, Brian Z
    Shibata, Kazuhiro
    Sugiura, Koji
    Takenaka, Yoichi
    Teasdale, Rohan D.
    Wells, Christine A.
    Zhu, Yunxia
    Kai, Chikatoshi
    Kawai, Jun
    Hume, David A.
    Carninci, Piero
    Hayashizaki, Yoshihide
    Griffith University Author(s)
    Wells, Christine
    Year published
    2006
    Metadata
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    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 ...
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    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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    Journal Title
    PLoS Genetics
    Volume
    2
    Issue
    4
    Publisher URI
    http://www.plosgenetics.org/home.action
    DOI
    https://doi.org/10.1371/journal.pgen.0020062
    Copyright Statement
    Copyright 2006 Maeda et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License CCAL. (http://www.plos.org/journals/license.html)
    Subject
    Genetics
    Publication URI
    http://hdl.handle.net/10072/20582.1
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    • Journal articles

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