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Functional annotation of a full-length mouse cDNA collection

Nature volume 409, pages 685–690 (2001)Cite this article

Abstract

The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

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Figure 1: Phase II full-insert sequencing flow chart.
Figure 2: The criteria used in assigning RIKEN definitions (riken_defs).

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Acknowledgements

We thank the following (in alphabetical order) for discussion, encouragement and technical assistance: R. Abagyan, T. Akimura, K. Arakawa, M. Boguski, L. Corbani, T. A. Dragani, J. T. Eppig, S. Fujimori, G. Grillo, T. Haga, T. Hanagaki, S. Hanaoka, S. Hatta, N. Hayatsu, K. Hiramoto, T. Hiraoka, T. Hirozane, Y. Hodoyama, F. Hori, T. Hubbard, R. Hynes, K. Ikeda, K. Ikeo, C. Imamura, K. Imotani, S. Inoue, H. Kato, N. Kikuchi, Y. Kojima, A. Konagaya, M. Kouda, S. Koya, M. Kubota, S. Kumagai, C. Kurihara, M. Kusakabe, F. Licciulli, S. Liuni, L. Maltais, T. Matsuyama, L. McKenzie, A. Miyazaki, K. Mori, M. Muramatsu, M. Nakamura, K. Nomura, N. Nukina, K. Numata, R. Numazaki, M. Ohno, Y. Okuma, H. Ono, C. Owa, Y. Ozawa, G. Pertea, S. Ramachandran, E. M. Rubin, N. Saga, H. Saitou, H. Sakai, C. Sakai, A. Sakurai, H. Sano, D. Sasaki, L. Sato, C. Schneider, J. Schug, T. Shiraki, M. B. Soares, Y. Sogabe, C. Stoeckert, H. Sugawara, R. Sultana, H. Suzuki, M. Tagami, A. Tagawa, F. Takahashi, S. Takaku-Akahira, M. Takeuchi, T. Tanaka, Y. Tateno, Y. Tejima, J. Todd, A. Tomaru, S. Tonegawa, T. Toya, A. Wada, L. Wagner, A. Watahiki, T. Yamamura, T. Yamashita, T. Yao, A. Yasunishi, T. Yokota, S. Yokoyama, A. Yoshiki and K. Yotsutani. We also thank N. Kazuta, Y. Sigemoto, H. Torigoe and T. Washida for secretarial assistance. This study has been mainly supported by a grant for the RIKEN Genome Exploration Research Project and CREST (Core Research for Evolutional Science and Technology) to Y.H. Further support came from ACT-JST (Research and Development for Applying Advanced Computational Science and Technology) of Japan Science and Technology Corporation (JST) to Y.H. and H.M., and the Science and Technology Agency of the Japanese Government to Y.H. and Y.O. (All funds from the Science Technology Agency of the Japanese Government.) This work was also supported by a Grant-in-Aid for Scientific Research on Priority Areas and Human Genome Program, from the Ministry of Education, Science and Culture, and by a Grant-in-Aid for a Second Term Comprehensive 10-Year Strategy for Cancer Control from the Ministry of Health and Welfare to Y.H. Authors’ contributions: J. Kawai and Y. Okazaki contributed as organizers in phase II team and FANTOM, respectively. A. Shinagawa and H. Bono contributed as managers in sequence data production system and computing system, respectively. J. Quackenbush, P. Carninci, M. J. Brownstein, D. A. Hume, C. Schönbach, H. Suzuki and C. Weitz acted as senior managers of the annotation project.

Author information

Authors and Affiliations

  1. Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan

    J. Kawai, A. Shinagawa, K. Shibata, M. Yoshino, M. Itoh, Y. Ishii, T. Arakawa, A. Hara, Y. Fukunishi, H. Konno, J. Adachi, S. Fukuda, K. Aizawa, M. Izawa, K. Nishi, H. Kiyosawa, S. Kondo, I. Yamanaka, T. Saito, Y. Okazaki, H. Bono, R. Saito, K. Kadota, K. Sakai, T. Okido, M. Furuno, H. Aono, P. Carninci, M. Kamiya, K. Sato, Y. Shibata, H. Suzuki, K. Yoshida & Y. Hayashizaki

  2. CREST, JST, 3-1-1 Koyadai, Tsukuba, 305-0074, Ibaraki, Japan

    J. Kawai, K. Shibata, M. Itoh, Y. Fukunishi, H. Konno, S. Fukuda, K. Aizawa, M. Kamiya & Y. Hayashizaki

  3. Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Shizuoka, Japan

    T. Gojobori & J. Mashima

  4. NTT Software Corporation, 223-1 Yamashita-cho, Naka-ku, Yokohama, 231-8554, Kanagawa, Japan

    T. Kasukawa, Y. Hasegawa, H. Kawaji & S. Kohtsuki

  5. Osaka University, 1-3 Machikaneyama, Toyonaka, 560-8531, Osaka, Japan

    H. Matsuda & H. Kawaji

  6. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK

    M. Ashburner & W. Fleischmann

  7. Genomics Institute of the Novartis Research Foundation, 3115 Merryfield Row, San Diego, 92121, California, USA

    S. Batalov & C. Fletcher

  8. The Coordinated Laboratory for Computational Genomics, University of Iowa Iowa City, 52242, Iowa, USA

    T. Casavant

  9. The Rockefeller University, 1230 York Avenue, New York, 10021-6399, New York, USA

    T. Gaasterland

  10. Dipartimento di Fisiologia e Biochimica Generali, Universita di Milano Via Celoria, 26, Milano, 20133, Italy

    C. Gissi & G. Pesole

  11. Mouse Genome Informatics, The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, Maine, USA

    B. King, R. Baldarelli, J. Blake, C. Bult, D. Hill & M. Ringwald

  12. Laboratory for Bioinformatics, Faculty of Environmental Information, Keio University, 5322 Endoh, Fujisawa, 252-0816, Kanagawa, Japan

    H. Kochiwa, R. Suzuki, M. Tomita & T. Washio

  13. Department of Molecular & Cell Biology, University of Maryland at Baltimore, Baltimore, 20201, Maryland, USA

    P. Kuehl

  14. Department of Molecular & Cell Biology, University of California, Berkeley, 142 Life Sciences Addition #3200, Berkeley, 94720-3200, California, USA

    S. Lewis

  15. Computational Proteomics Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan

    Y. Matsuo

  16. Tokai University, Graduate School of Marine Science and Technology, 3-20-1 Orido, Shimizu, 424-8610, Shizuoka, Japan

    I. Nikaido

  17. The Institute for Genomic Research, 9712 Medical Center Dr., Rockville, 20850, Maryland, USA

    J. Quackenbush & N. H. Lee

  18. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 8N805, Bethesda, 20894, Maryland, USA

    L. M. Schriml & L. Wagner

  19. LION Bioscience AG, Im Neuenheimer Feld 515-519, Heidelberg, D-69120, Germany

    F. Staubli, N. Bojunga & M. Hofmann

  20. Stanford University School of Medicine, Beckman Centre B271A, Stanford, 94305-5428, California, USA

    G. Barsh

  21. Lawrence Berkeley Laboratory, 1 Cyclotron Rd, MS84-255, Berkeley, 94710, California, USA

    D. Boffelli

  22. Department of Pediatrics, The University of Iowa, 200 Hawkins Drive 440B EMRB, Iowa City, 52242-1009, Iowa, USA

    M. F. de Bonaldo

  23. Laboratory of Genetics, NIMH/NHGRI, National Institutes of Health Building 36, Room 3D06, Bethesda, 20892, Maryland, USA

    M. J. Brownstein

  24. Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-8655, Tokyo, Japan

    M. Fujita

  25. Istituto Tumori Milano, Via Venezian,1, Milano, 120133, Italy

    M. Gariboldi

  26. Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, 02115, Massachusetts, USA

    S. Gustincich

  27. Institute for Molecular Bioscience, University of Queensland, Brisbane, 4072, Queensland, Australia

    D. A. Hume

  28. Department of Medical Genetics, Wellcome Trust Centre for Molecular Mechanisms in Disease, University of Cambridge, Wellcome Trust/MRC building, Addenbrookes Hospital, Cambridge, CB2 2XY, UK

    P. Lyons

  29. LNCIB c/o AREA Science Park, Padriciano 99, Trieste, 34012, Italy

    L. Marchionni

  30. Computational and Bioinformatics Laboratory, Center for Bioinformatics, University of Pennsylvania, 1313 Blockley Hall, 418 Guardian Drive, Philadelphia, 19104-6021, Pennsylvania, USA

    J. Mazzarelli

  31. Vertebrate Developmental Neurogenetics, The Rockefeller University, 1230 York Avenue, Box 242, New York, 10021-6399, New York, USA

    P. Mombaerts & I. Rodriguez

  32. University at Buffalo/Roswell Park Cancer Institute, 120 Meyers Rd.#615, Amherst, 14226, New York, USA

    P. Nordone

  33. Department of Genetics, Stanford University, Beckman Centre B281, Stanford, 94305, California, USA

    B. Ring

  34. RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, 351-0198, Saitama, Japan

    N. Sakamoto

  35. National Cancer Research Institute, 1-1 Tsukiji, Chuo-ku, 104-0045, Tokyo, Japan

    H. Sasaki

  36. Computational Genomics Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan

    C. Schönbach

  37. Osaka Medical Center for Cancer, Nakamichi 1-3-3, Higashinari-ku, 537-8511, Osaka, Japan

    T. Seya

  38. Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, 02115, Massachusetts, USA

    K.-F. Storch & C. Weitz

  39. Department of Pediatrics, University of California, San Diego, School of Medicine, 9500 Gilman Dr., Medical Teaching Facility 253, La Jolla, 92093-0627, California, USA

    K. Toyo-oka

  40. E17-353, Center for Learning and Memory, Massacusetts Institute of Technlogy, 77 Massachusetts Ave., Cambridge, 02139, Massachusetts, USA

    K. H. Wang

  41. Massachusetts Institute of Technology, MIT CCR, 77 Massachusetts Avenue 17-230, Cambridge, 02139, Massachusetts, USA

    C. Whittaker

  42. Sanger Centre, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK

    L. Wilming

  43. University of California San Diego School of Medicine, 9500 Gilman Dr., Medical Teaching Facility, Room 252, La Jolla, 92093-0627, California, USA

    A. Wynshaw-Boris

  44. Tsukuba University, 1-1-1 Tennodai, Tsukuba, 305-8577,, Ibaraki, Japan

    K. Sato & Y. Hayashizaki

Consortia

The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium

  • The RIKEN Genome Exploration Research Group Phase II Team

    • J. Kawai
    • , A. Shinagawa
    • , K. Shibata
    • , M. Yoshino
    • , M. Itoh
    • , Y. Ishii
    • , T. Arakawa
    • , A. Hara
    • , Y. Fukunishi
    • , H. Konno
    • , J. Adachi
    • , S. Fukuda
    • , K. Aizawa
    • , M. Izawa
    • , K. Nishi
    • , H. Kiyosawa
    • , S. Kondo
    • , I. Yamanaka
    •  & T. Saito

  • FANTOM Consortium

    • Y. Okazaki
    • , T. Gojobori
    • , H. Bono
    • , T. Kasukawa
    • , R. Saito
    • , K. Kadota
    • , H. Matsuda
    • , M. Ashburner
    • , S. Batalov
    • , T. Casavant
    • , W. Fleischmann
    • , T. Gaasterland
    • , C. Gissi
    • , B. King
    • , H. Kochiwa
    • , P. Kuehl
    • , S. Lewis
    • , Y. Matsuo
    • , I. Nikaido
    • , G. Pesole
    • , J. Quackenbush
    • , L. M. Schriml
    • , F. Staubli
    • , R. Suzuki
    • , M. Tomita
    • , L. Wagner
    • , T. Washio
    • , K. Sakai
    • , T. Okido
    • , M. Furuno
    • , H. Aono
    • , R. Baldarelli
    • , G. Barsh
    • , J. Blake
    • , D. Boffelli
    • , N. Bojunga
    • , P. Carninci
    • , M. F. de Bonaldo
    • , M. J. Brownstein
    • , C. Bult
    • , C. Fletcher
    • , M. Fujita
    • , M. Gariboldi
    • , S. Gustincich
    • , D. Hill
    • , M. Hofmann
    • , D. A. Hume
    • , M. Kamiya
    • , N. H. Lee
    • , P. Lyons
    • , L. Marchionni
    • , J. Mashima
    • , J. Mazzarelli
    • , P. Mombaerts
    • , P. Nordone
    • , B. Ring
    • , M. Ringwald
    • , I. Rodriguez
    • , N. Sakamoto
    • , H. Sasaki
    • , K. Sato
    • , C. Schönbach
    • , T. Seya
    • , Y. Shibata
    • , K.-F. Storch
    • , H. Suzuki
    • , K. Toyo-oka
    • , K. H. Wang
    • , C. Weitz
    • , C. Whittaker
    • , L. Wilming
    • , A. Wynshaw-Boris
    • , K. Yoshida
    • , Y. Hasegawa
    • , H. Kawaji
    •  & S. Kohtsuki

  • General organizer

    • Y. Hayashizaki

Corresponding author

Correspondence to Y. Hayashizaki.

Supplementary information

Supplementary Figure 1

A Distribution of the length of 21,076 insert DNAs (DOC 34 kb)

B Sequence accuracy

Supplementary Figure 2

A SAP domain containing RIKEN clones (DOC 41 kb)

B Phylogenetic tree of the known OATPs and RIKEN clones

Supplementary Figure 3

Alignment of the amino acid sequences of the known OATPs (DOC 135 kb)

Supplementary Figure 4

Mapping of RIKEN clones using Radiation Hybrid (DOC 31 kb)

Supplementary Table 1

DDBJ accsession number and MGI ID for RIKEN ID (TXT 801 kb)

Supplementary Table 2

A Full-length evaluation (DOC 80 kb)

B Analysis of Alternative Splicing in Redundant Clone Set

Supplementary Table 3 (DOC 1026 kb)

Supplementary Table 4

A RIKEN clones containing a DSP domain (DOC 997 kb)

B RIKEN clones containing a consensus kinase signature motif

C InterPro Motifs in RIKEN clones

Supplementary Table 5

A Motifs identified by maximum density subgraph analysis (DOC 64 kb)

B UTR Functional Elements

Supplementary Table 6

RH Map of RIKEN Clones using RH databases (DOC 56 kb)

Supplementary Table 7

A Databases that were used for the functional annotation (DOC 82 kb)

B Software that was used during full-length sequencing and the functional annotation

Supplementary Table 8

Strategies of Gene Ontology Assignment (DOC 32 kb)

Supplementary methods

This information is also available at: http://www.gsc.riken.go.jp/e/FANTOM/supplement/ (DOC 32 kb)

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The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium. Functional annotation of a full-length mouse cDNA collection. Nature 409, 685–690 (2001). https://doi.org/10.1038/35055500

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  • DOI: https://doi.org/10.1038/35055500

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