Searching journal content for articles similar to Forrest et al. 13 (6b): 1366.

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  1. 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
    ...topic (e.g., only protein interactions or only disease associations). At the time of annotating and analyzing 60,000 RIKEN mouse FANTOM2 cDNA clones ( The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team 2002 ; Mouse Genome Sequencing Consortium 2002 ), none...
  2. LETTER: The Comparative Proteomics of Ubiquitination in Mouse
    • Colin A.M. Semple,
    • RIKEN GER Group,
    • and GSL Members
    Genome Res. June 2003 13: 1389-1394; doi:10.1101/gr.980303
    ...and Eldridge 2002 ). The large numbers of proteins containing these domains mean that a huge number of different E3 complexes, recognizing a wide range of protein substrates, can be formed. The Representative Transcript and Protein Set (RTPS) amalgamates cDNA clones produced in the recent RIKEN FANTOM2 project...
  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
    ...and The RIKEN Genome Exploration Research Group Phase I and II Team, 2002 ). In addition to the large collection of novel protein-coding transcripts, the FANTOM2 transcript set revealed many nonprotein-coding RNAs (ncRNAs) ( Numata et al. 2003 ) and disease genes, a subset of which are included among 7260 pairs...
  4. 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
    ...a nonredundant protein set (RPS), which combines public sequences with high-quality representative sequences from the FANTOM2 data set. We again used InterPro domain annotations to extract sequences from RPS3 (nonredundant representative protein set 3, available from RIKEN, http://fantom2.gsc.riken...
  5. LETTER: Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage
    • Christine A. Wells,
    • Timothy Ravasi,
    • Razvan Sultana,
    • Ken Yagi,
    • Piero Carninci,
    • Hidemasa Bono,
    • Geoffrey Faulkner,
    • Yasushi Okazaki,
    • John Quackenbush,
    • David A. Hume,
    • RIKEN GER Group,
    • GSL Members,
    • and Paul A. Lyons
    Genome Res. June 2003 13: 1360-1365; doi:10.1101/gr.1056103
    ...(GO) classifications, and were derived from the RIKEN FANTOM2 database (macrophage restricted set) as described previously ( Okazaki et al. 2002 ), and from UniGene assignments (LPS inducible set), interrogated using the Stanford SOURCE batch server ( http://-www5.stanford...
  6. 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
    ...peptides within the PROCREST predicted ORFs of the RIKEN 60,770 FANTOM2 cDNA clone set and the mouse secretome. The total numbers of proteins within 50 amino acid blocks are plotted. One reason for the large number of predicted putative short secreted proteins was that several mouse DNA repeat sequences...
  7. 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
    ...and GSL Members, and Grimmond, S. 2003b . Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set. Genome Res. (this issue). ↵ Furuno, M., Kasukawa, T., Saito, R., Adachi, J., Suzuki, H., Baldarelli, R., Hayashizaki, Y., and Okazaki, Y. 2003 . CDS annotation in full-length c...
  8. LETTER: Identification of Mammalian microRNA Host Genes and Transcription Units
    • Antony Rodriguez,
    • Sam Griffiths-Jones,
    • Jennifer L. Ashurst,
    • and Allan Bradley
    Genome Res. October 2004 14: 1902-1910; Published in Advance September 13, 2004, doi:10.1101/gr.2722704
    .... 2004 ) was used to determine if any GO terms are significantly overrepre sented in microRNA host genes. mRNA-Like Noncoding RNA Databases A total of ∼10,000 mlncRNAs sequences were collected from the FANTOM Functional Annotation Database ( http://fantom2.gsc.riken.go.jp/ ; Numata et al. 2003...
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