Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs

Norihiro Maeda*, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G. Engström, Boris Lenhard, Rajith N. Aturaliya, Serge Batalov, Kirk W. Beisel, Carol J. Bult, Colin F. Fletcher, Alistair R.R. Forrest, Masaaki Furuno, David Hill, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Shintaro Katayama, Masaru Katoh, Tsugumi KawashimaJohn Quackenbushb, Timothy Ravasi, Brian Z. Ring, Kazuhiro Shibata, Koji Sugiura, Yoichi Takenaka, Rohan D. Teasdale, Christine A. Wells, Yunxia Zhu, Chikatoshi Kai, Jun Kawai, David A. Hume, Piero Carninci, Yoshihide Hayashizaki

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

146 Scopus citations


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.

Original languageEnglish (US)
Article numbere62
Pages (from-to)498-503
Number of pages6
JournalPLoS Genetics
Issue number4
StatePublished - Apr 2006
Externally publishedYes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research


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