Searching journal content for articles similar to Hayashizaki 13 (6b): 1265.

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  1. 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
    ...G Protein-Coupled Receptor Genes in the FANTOM2 Database Yuka Kawasawa 1 , 6 , Louise M. McKenzie 2 , David P. Hill 2 , Hidemasa Bono 3 , RIKEN GER Group 3 , GSL Members 4 , 5 , and Masashi Yanagisawa 1...
  2. LETTER: CDS Annotation in Full-Length cDNA Sequence
    • Masaaki Furuno,
    • Takeya Kasukawa,
    • Rintaro Saito,
    • Jun Adachi,
    • Harukazu Suzuki,
    • Richard Baldarelli,
    • Yoshihide Hayashizaki,
    • and Yasushi Okazaki
    Genome Res. June 2003 13: 1478-1487; doi:10.1101/gr.1060303
    ...DNA (HTC) sequences, such as the set of 60,770 cDNAs isolated from full-length enriched libraries of the FANTOM2 project. We developed a CDS annotation strategy that uses a variety of different CDS prediction programs to annotate the CDS regions of FANTOM2 cDNAs. These include rsCDS, which uses...
  3. LETTER: Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling
    • Itoshi Nikaido,
    • Chika Saito,
    • Yosuke Mizuno,
    • Makiko Meguro,
    • Hidemasa Bono,
    • Moritoshi Kadomura,
    • Tomohiro Kono,
    • Gerard A. Morris,
    • Paul A. Lyons,
    • Mitsuo Oshimura,
    • RIKEN GER Group,
    • GSL Members,
    • Yoshihide Hayashizaki,
    • and Yasushi Okazaki
    Genome Res. June 2003 13: 1402-1409; doi:10.1101/gr.1055303
    .... Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res. (this issue). ↵ Kumar, M. and Carmichael, G.G. 1998 . Antisense RNA: Function and fate of duplex RNA in cells of higher eukaryotes. Microbiol. Mol. Biol. Rev. 62 : 1415 -1434. ↵ MacDonald, H.R. and Wevrick...
  4. 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
    ...in the FANTOM2 meeting (April 29 to May 5, 2002, Yokohama, Japan), which is the basis of this special issue of Genome Research . The History of FANTOM The FANTOM ( F unctional An no t ation o f M ouse) Consortium is a group of molecular biologists from the RIKEN Genomic Sciences Center in Yokohama, elsewhere...
  5. 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
    ...with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools to circumvent some...
  6. LETTER: Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays
    • Hidemasa Bono,
    • Ken Yagi,
    • Takeya Kasukawa,
    • Itoshi Nikaido,
    • Naoko Tominaga,
    • Rika Miki,
    • Yosuke Mizuno,
    • Yasuhiro Tomaru,
    • Hitoshi Goto,
    • Hiroyuki Nitanda,
    • Daisuke Shimizu,
    • Hirochika Makino,
    • Tomoyuki Morita,
    • Junshin Fujiyama,
    • Takehito Sakai,
    • Takashi Shimoji,
    • David A. Hume,
    • RIKEN GER Group,
    • GSL Members,
    • Yoshihide Hayashizaki,
    • and Yasushi Okazaki
    Genome Res. June 2003 13: 1318-1323; doi:10.1101/gr.1075103
    ...of functional genomics. In this report, we determine the expression profile of 57,931 clones on 20 mouse tissues using cDNA microarrays. Of these 57,931 clones, 22,928 clones correspond to the FANTOM2 clone set. The set represents 20,234 transcriptional units (TUs) out of 33,409 TUs in the FANTOM2 set. We...
  7. LETTER: Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse
    • Alistair R.R. Forrest,
    • Timothy Ravasi,
    • Darrin Taylor,
    • Thomas Huber,
    • David A. Hume,
    • RIKEN GER Group,
    • GSL Members,
    • and Sean Grimmond
    Genome Res. June 2003 13: 1443-1454; doi:10.1101/gr.954803
    ...in good agreement with previous schemes and allowed us to demonstrate domain associations with a number of clusters. Finally, we comment on the complementary nature of cDNA and genome-based gene detection and the impact of the FANTOM2 transcriptome project. Footnotes [Supplemental...
  8. 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 c...
  9. ARTICLE: Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome
    • Mihaela Zavolan,
    • Shinji Kondo,
    • Christian Schönbach,
    • Jun Adachi,
    • David A. Hume,
    • RIKEN GER Group,
    • GSL Members,
    • Yoshihide Hayashizaki,
    • and Terry Gaasterland
    Genome Res. June 2003 13: 1290-1300; doi:10.1101/gr.1017303
    ...351-0198, Japan Abstract We analyzed the FANTOM2 clone set of 60,770 RIKEN full-length mouse cDNA sequences and 44,122 public mRNA sequences. We developed a new computational procedure to identify and classify the forms of splice variation evident in this data set and organized...
  10. Methods: DNA Book
    • Jun Kawai and
    • Yoshihide Hayashizaki
    Genome Res. June 2003 13: 1488-1495; doi:10.1101/gr.914203
    ...and distribution of scientific information, including nucleotide sequences and gene annotation, as well as scientific papers. The RIKEN FANTOM database of sequences and annotation has been released and is accessible through the Internet ( http://fantom2.gsc.riken.go.jp/ ). Leading to this, a different situation...
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