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dc.contributor.authorMaeda, Norihiro
dc.contributor.authorKasukawa, Takeya
dc.contributor.authorOyama, Rieko
dc.contributor.authorGough, Julian
dc.contributor.authorFrith, Martin
dc.contributor.authorEngstrom, Par
dc.contributor.authorLenhard, Boris
dc.contributor.authorAturaliya, Rajith
dc.contributor.authorBatalov, Serge
dc.contributor.authorBeisel, Kirk W
dc.contributor.authorBult, Carol J
dc.contributor.authorFletcher, Colin F
dc.contributor.authorForrest, Alistair Raymond Russell
dc.contributor.authorFuruno, Masaaki
dc.contributor.authorHill, David
dc.contributor.authorItoh, Masayoshi
dc.contributor.authorKanamori-Katayama, Mutsumi
dc.contributor.authorKatayama, Shintaro
dc.contributor.authorKatoh, Masaru
dc.contributor.authorKawashima, Tsugumi
dc.contributor.authorQuackenbush, John
dc.contributor.authorRavasi, Timothy
dc.contributor.authorRing, Brian Z
dc.contributor.authorShibata, Kazuhiro
dc.contributor.authorSugiura, Koji
dc.contributor.authorTakenaka, Yoichi
dc.contributor.authorTeasdale, Rohan D.
dc.contributor.authorWells, Christine A.
dc.contributor.authorZhu, Yunxia
dc.contributor.authorKai, Chikatoshi
dc.contributor.authorKawai, Jun
dc.contributor.authorHume, David A.
dc.contributor.authorCarninci, Piero
dc.contributor.authorHayashizaki, Yoshihide
dc.description.abstractThe 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.
dc.format.extent237534 bytes
dc.publisherPublic Library of Science
dc.publisher.placeUnited States
dc.relation.ispartofjournalPLoS Genetics
dc.titleTranscript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
dc.typeJournal article
dc.type.descriptionC1 - Articles
gro.facultyEskitis, Inst Cell&Molecular Therapies
gro.rights.copyrightCopyright 2006 Maeda et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License CCAL. (
gro.hasfulltextNo Full Text
gro.griffith.authorWells, Christine

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