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LETTER: G Protein-Coupled Receptor Genes in the FANTOM2 Database
- Yuka Kawasawa,
- Louise M. McKenzie,
- David P. Hill,
- Hidemasa Bono,
- RIKEN GER Group,
- GSL Members,
- and Masashi Yanagisawa
Genome Res. June 2003 13: 1466-1477; doi:10.1101/gr.1087603
.... 2001 ). The second phase of this project (FANTOM2) resulted in an additional 39,694-cDNA set (total 60,770) and a more global analysis of the mouse transcriptome ( The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I and II Team 2002 ). Along with the achievement of the mouse...
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RESOURCE: Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS
- Takeshi Nagashima,
- Diego G. Silva,
- Nikolai Petrovsky,
- Luis A. Socha,
- Harukazu Suzuki,
- Rintaro Saito,
- Takeya Kasukawa,
- Igor V. Kurochkin,
- Akihiko Konagaya,
- and Christian Schönbach
Genome Res. June 2003 13: 1520-1533; doi:10.1101/gr.1019903
...Retrieval The FACTS system was applied to both the computational and human annotated FANTOM2 cDNA clone set (Suppl. 3). Here, we report only the results for human curated clones. The coverage and specificity of abstract retrieval from MEDLINE using gene or protein names depends on how queries are formulated...
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RESOURCE: Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
- Takeya Kasukawa,
- Masaaki Furuno,
- Itoshi Nikaido,
- Hidemasa Bono,
- David A. Hume,
- Carol Bult,
- David P. Hill,
- Richard Baldarelli,
- Julian Gough,
- Alexander Kanapin,
- Hideo Matsuda,
- Lynn M. Schriml,
- Yoshihide Hayashizaki,
- Yasushi Okazaki,
- and John Quackenbush
Genome Res. June 2003 13: 1542-1551; doi:10.1101/gr.992803
...problems of large-scale annotation, and devised computational interfaces to expedite human curation. As we began to prepare for the much larger task of annotating the 60,770-clone FANTOM2 cDNA set, which was to include reannotation of the original FANTOM1 clones to provide the best and most current...
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LETTER: Kinesin Superfamily Proteins (KIFs) in the Mouse Transcriptome
- Harukata Miki,
- Mitsutoshi Setou,
- RIKEN GER Group,
- GSL Members,
- and Nobutaka Hirokawa
Genome Res. June 2003 13: 1455-1465; doi:10.1101/gr.984503
...for intracellular transport. We report the comprehensive analysis of the Kinesin Superfamily, which is the first and only large protein family whose constituents have been completely identified and confirmed in silico and at the cDNA, mRNA level. In FANTOM2, we have found 90 clones from 33 Kinesin Superfamily...
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RESOURCE: Connecting Sequence and Biology in the Laboratory Mouse
- Richard M. Baldarelli,
- David P. Hill,
- Judith A. Blake,
- Jun Adachi,
- Masaaki Furuno,
- Dirck Bradt,
- Lori E. Corbani,
- Sharon Cousins,
- Kenneth S. Frazer,
- Dong Qi,
- Longlong Yang,
- Sridhar Ramachandran,
- Deborah Reed,
- Yunxia Zhu,
- Takeya Kasukawa,
- Martin Ringwald,
- Benjamin L. King,
- Lois J. Maltais,
- Louise M. McKenzie,
- Lynn M. Schriml,
- Donna Maglott,
- Deanna M. Church,
- Kim Pruitt,
- Janan T. Eppig,
- Joel E. Richardson,
- Jim A. Kadin,
- and Carol J. Bult
Genome Res. June 2003 13: 1505-1519; doi:10.1101/gr.991003
...clone set, describing the computational and manual curation methods used to distill information from the sequences for 60,770 FANTOM2 cDNA clones to information for 19,980 mouse genes. We discuss how this serves as an entry point to the process by which the MGI and LocusLink/RefSeq groups join sequence...
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LETTER: The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment
- Sean M. Grimmond,
- Kevin C. Miranda,
- Zheng Yuan,
- Melissa J. Davis,
- David A. Hume,
- Ken Yagi,
- Naoko Tominaga,
- Hidemasa Bono,
- Yoshihide Hayashizaki,
- Yasushi Okazaki,
- RIKEN GER Group,
- GSL Members,
- and Rohan D. Teasdale
Genome Res. June 2003 13: 1350-1359; doi:10.1101/gr.983703
...considered as candidates for inclusion within the mouse secretome. View this table: In this window In a new window Table 1. Origin of Proteins Within the Mouse Secretome The initial analysis for ORFs in the 60,770 FANTOM2 clone set, using the PROCREST algorithm, identified a large number of cDNAs...
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LETTER: Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome
- Timothy Ravasi,
- Thomas Huber,
- Mihaela Zavolan,
- Alistair Forrest,
- Terry Gaasterland,
- Sean Grimmond,
- RIKEN GER Group,
- GSL Members,
- and David A. Hume
Genome Res. June 2003 13: 1430-1442; doi:10.1101/gr.949803
...distinct zinc finger proteins. The RIKEN full-length, Representative Transcript and Protein Set (RTPS), represents the most complete transcriptome available in higher eukaryotes. The full-length cDNA and protein sequences allow us to better map each individual transcript to the mouse and define human...
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RESOURCE: GeneLynx Mouse: Integrated Portal to the Mouse Genome
- Boris Lenhard,
- Claes Wahlestedt,
- and Wyeth W. Wasserman
Genome Res. June 2003 13: 1501-1504; doi:10.1101/gr.951403
...on the Fantom2 collection of 60770 mouse full-length cDNAs. In addition to the popular functionality of the human portal, GeneLynx Mouse introduces a novel set of features to facilitate comparisons between orthologous mouse and human genes. RESULTS AND DISCUSSION Gene-Based Clusters GeneLynx Mouse (release 1...
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COMMENTARY: A Guide to the Mammalian Genome
- Yasushi Okazaki and
- David A. Hume
Genome Res. June 2003 13: 1267-1272; doi:10.1101/gr.1445603
...mouse orthologs: Exploration of the FANTOM2 cDNA sequence data set. Genome Res. (this issue). ↵ Semple, C.A.M., and RIKEN GER Group and GSL Members. 2003 . The comparative proteomics of ubiquitination in mouse. Genome Res. (this issue). Silva, D.G., Schönbach, C., Brusic, V., Socha, L.A., Nagashima, T...

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