Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Y. Okazaki, M. Furuno, T. Kasukawa, J. Adachi, H. Bono, S. Kondo, I. Nikaido, N. Osato, R. Saito, H. Suzuki, I. Yamanaka, H. Kiyosawa, K. Yagi, Y. Tomaru, Y. Hasegawa, A. Nogami, C. Schönbach, T. Gojobori, R. Baldarelli, D. P. HillC. Bult, D. A. Hume, J. Quackenbush, L. M. Schriml, A. Kanapin, H. Matsuda, S. Batalov, Kirk Beisel, J. A. Blake, D. Bradt, V. Brusic, C. Chothia, L. E. Corbani, S. Cousins, E. Dalla, T. A. Dragani, C. F. Fletcher, A. Forrest, K. S. Frazer, T. Gaasterland, M. Gariboldi, C. Gissi, A. Godzik, J. Gough, S. Grimmond, S. Gustincich, N. Hirokawa, I. J. Jackson, E. D. Jarvis, A. Kanai, H. Kawaji, Y. Kawasawa, R. M. Kedzierski, B. L. King, A. Konagaya, I. V. Kurochkin, Y. Lee, B. Lenhard, P. A. Lyons, D. R. Maglott, L. Maltais, L. Marchionni, L. McKenzie, H. Miki, T. Nagashima, K. Numata, T. Okido, W. J. Pavan, G. Pertea, G. Pesole, N. Petrovsky, R. Pillai, J. U. Pontius, D. Qi, S. Ramachandran, T. Ravasi, J. C. Reed, D. J. Reed, J. Reid, B. Z. Ring, M. Ringwald, A. Sandelin, C. Schneider, C. A M Semple, M. Setou, K. Shimada, R. Sultana, Y. Takenaka, M. S. Taylor, R. D. Teasdale, M. Tomita, R. Verardo, L. Wagner, C. Wahlestedt, Y. Wang, Y. Watanabe, C. Wells, L. G. Wilming, A. Wynshaw-Boris, M. Yanagisawa, I. Yang, L. Yang, Z. Yuan, M. Zavolan, Y. Zhu, A. Zimmer, P. Carninci, N. Hayatsu, T. Hirozane-Kishikawa, H. Konno, M. Nakamura, N. Sakazume, K. Sato, T. Shiraki, K. Waki, J. Kawai, K. Aizawa, T. Arakawa, S. Fukuda, A. Hara, W. Hashizume, K. Imotani, Y. Ishii, M. Itoh, I. Kagawa, A. Miyazaki, K. Sakai, D. Sasaki, K. Shibata, A. Shinagawa, A. Yasunishi, M. Yoshino, R. Waterston, E. S. Lander, J. Rogers, E. Birney, Y. Hayashizaki

Research output: Contribution to journalArticle

1191 Citations (Scopus)

Abstract

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Original languageEnglish
Pages (from-to)563-573
Number of pages11
JournalNature
Volume420
Issue number6915
DOIs
StatePublished - Dec 5 2002

Fingerprint

Gene Expression Profiling
Complementary DNA
Transcriptome
Clone Cells
Untranslated RNA
Messenger RNA
Proteins
Alternative Splicing
Genomics
Genome
Databases

All Science Journal Classification (ASJC) codes

  • General

Cite this

Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., ... Hayashizaki, Y. (2002). Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420(6915), 563-573. https://doi.org/10.1038/nature01266

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. / Okazaki, Y.; Furuno, M.; Kasukawa, T.; Adachi, J.; Bono, H.; Kondo, S.; Nikaido, I.; Osato, N.; Saito, R.; Suzuki, H.; Yamanaka, I.; Kiyosawa, H.; Yagi, K.; Tomaru, Y.; Hasegawa, Y.; Nogami, A.; Schönbach, C.; Gojobori, T.; Baldarelli, R.; Hill, D. P.; Bult, C.; Hume, D. A.; Quackenbush, J.; Schriml, L. M.; Kanapin, A.; Matsuda, H.; Batalov, S.; Beisel, Kirk; Blake, J. A.; Bradt, D.; Brusic, V.; Chothia, C.; Corbani, L. E.; Cousins, S.; Dalla, E.; Dragani, T. A.; Fletcher, C. F.; Forrest, A.; Frazer, K. S.; Gaasterland, T.; Gariboldi, M.; Gissi, C.; Godzik, A.; Gough, J.; Grimmond, S.; Gustincich, S.; Hirokawa, N.; Jackson, I. J.; Jarvis, E. D.; Kanai, A.; Kawaji, H.; Kawasawa, Y.; Kedzierski, R. M.; King, B. L.; Konagaya, A.; Kurochkin, I. V.; Lee, Y.; Lenhard, B.; Lyons, P. A.; Maglott, D. R.; Maltais, L.; Marchionni, L.; McKenzie, L.; Miki, H.; Nagashima, T.; Numata, K.; Okido, T.; Pavan, W. J.; Pertea, G.; Pesole, G.; Petrovsky, N.; Pillai, R.; Pontius, J. U.; Qi, D.; Ramachandran, S.; Ravasi, T.; Reed, J. C.; Reed, D. J.; Reid, J.; Ring, B. Z.; Ringwald, M.; Sandelin, A.; Schneider, C.; Semple, C. A M; Setou, M.; Shimada, K.; Sultana, R.; Takenaka, Y.; Taylor, M. S.; Teasdale, R. D.; Tomita, M.; Verardo, R.; Wagner, L.; Wahlestedt, C.; Wang, Y.; Watanabe, Y.; Wells, C.; Wilming, L. G.; Wynshaw-Boris, A.; Yanagisawa, M.; Yang, I.; Yang, L.; Yuan, Z.; Zavolan, M.; Zhu, Y.; Zimmer, A.; Carninci, P.; Hayatsu, N.; Hirozane-Kishikawa, T.; Konno, H.; Nakamura, M.; Sakazume, N.; Sato, K.; Shiraki, T.; Waki, K.; Kawai, J.; Aizawa, K.; Arakawa, T.; Fukuda, S.; Hara, A.; Hashizume, W.; Imotani, K.; Ishii, Y.; Itoh, M.; Kagawa, I.; Miyazaki, A.; Sakai, K.; Sasaki, D.; Shibata, K.; Shinagawa, A.; Yasunishi, A.; Yoshino, M.; Waterston, R.; Lander, E. S.; Rogers, J.; Birney, E.; Hayashizaki, Y.

In: Nature, Vol. 420, No. 6915, 05.12.2002, p. 563-573.

Research output: Contribution to journalArticle

Okazaki, Y, Furuno, M, Kasukawa, T, Adachi, J, Bono, H, Kondo, S, Nikaido, I, Osato, N, Saito, R, Suzuki, H, Yamanaka, I, Kiyosawa, H, Yagi, K, Tomaru, Y, Hasegawa, Y, Nogami, A, Schönbach, C, Gojobori, T, Baldarelli, R, Hill, DP, Bult, C, Hume, DA, Quackenbush, J, Schriml, LM, Kanapin, A, Matsuda, H, Batalov, S, Beisel, K, Blake, JA, Bradt, D, Brusic, V, Chothia, C, Corbani, LE, Cousins, S, Dalla, E, Dragani, TA, Fletcher, CF, Forrest, A, Frazer, KS, Gaasterland, T, Gariboldi, M, Gissi, C, Godzik, A, Gough, J, Grimmond, S, Gustincich, S, Hirokawa, N, Jackson, IJ, Jarvis, ED, Kanai, A, Kawaji, H, Kawasawa, Y, Kedzierski, RM, King, BL, Konagaya, A, Kurochkin, IV, Lee, Y, Lenhard, B, Lyons, PA, Maglott, DR, Maltais, L, Marchionni, L, McKenzie, L, Miki, H, Nagashima, T, Numata, K, Okido, T, Pavan, WJ, Pertea, G, Pesole, G, Petrovsky, N, Pillai, R, Pontius, JU, Qi, D, Ramachandran, S, Ravasi, T, Reed, JC, Reed, DJ, Reid, J, Ring, BZ, Ringwald, M, Sandelin, A, Schneider, C, Semple, CAM, Setou, M, Shimada, K, Sultana, R, Takenaka, Y, Taylor, MS, Teasdale, RD, Tomita, M, Verardo, R, Wagner, L, Wahlestedt, C, Wang, Y, Watanabe, Y, Wells, C, Wilming, LG, Wynshaw-Boris, A, Yanagisawa, M, Yang, I, Yang, L, Yuan, Z, Zavolan, M, Zhu, Y, Zimmer, A, Carninci, P, Hayatsu, N, Hirozane-Kishikawa, T, Konno, H, Nakamura, M, Sakazume, N, Sato, K, Shiraki, T, Waki, K, Kawai, J, Aizawa, K, Arakawa, T, Fukuda, S, Hara, A, Hashizume, W, Imotani, K, Ishii, Y, Itoh, M, Kagawa, I, Miyazaki, A, Sakai, K, Sasaki, D, Shibata, K, Shinagawa, A, Yasunishi, A, Yoshino, M, Waterston, R, Lander, ES, Rogers, J, Birney, E & Hayashizaki, Y 2002, 'Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs', Nature, vol. 420, no. 6915, pp. 563-573. https://doi.org/10.1038/nature01266
Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 5;420(6915):563-573. https://doi.org/10.1038/nature01266
Okazaki, Y. ; Furuno, M. ; Kasukawa, T. ; Adachi, J. ; Bono, H. ; Kondo, S. ; Nikaido, I. ; Osato, N. ; Saito, R. ; Suzuki, H. ; Yamanaka, I. ; Kiyosawa, H. ; Yagi, K. ; Tomaru, Y. ; Hasegawa, Y. ; Nogami, A. ; Schönbach, C. ; Gojobori, T. ; Baldarelli, R. ; Hill, D. P. ; Bult, C. ; Hume, D. A. ; Quackenbush, J. ; Schriml, L. M. ; Kanapin, A. ; Matsuda, H. ; Batalov, S. ; Beisel, Kirk ; Blake, J. A. ; Bradt, D. ; Brusic, V. ; Chothia, C. ; Corbani, L. E. ; Cousins, S. ; Dalla, E. ; Dragani, T. A. ; Fletcher, C. F. ; Forrest, A. ; Frazer, K. S. ; Gaasterland, T. ; Gariboldi, M. ; Gissi, C. ; Godzik, A. ; Gough, J. ; Grimmond, S. ; Gustincich, S. ; Hirokawa, N. ; Jackson, I. J. ; Jarvis, E. D. ; Kanai, A. ; Kawaji, H. ; Kawasawa, Y. ; Kedzierski, R. M. ; King, B. L. ; Konagaya, A. ; Kurochkin, I. V. ; Lee, Y. ; Lenhard, B. ; Lyons, P. A. ; Maglott, D. R. ; Maltais, L. ; Marchionni, L. ; McKenzie, L. ; Miki, H. ; Nagashima, T. ; Numata, K. ; Okido, T. ; Pavan, W. J. ; Pertea, G. ; Pesole, G. ; Petrovsky, N. ; Pillai, R. ; Pontius, J. U. ; Qi, D. ; Ramachandran, S. ; Ravasi, T. ; Reed, J. C. ; Reed, D. J. ; Reid, J. ; Ring, B. Z. ; Ringwald, M. ; Sandelin, A. ; Schneider, C. ; Semple, C. A M ; Setou, M. ; Shimada, K. ; Sultana, R. ; Takenaka, Y. ; Taylor, M. S. ; Teasdale, R. D. ; Tomita, M. ; Verardo, R. ; Wagner, L. ; Wahlestedt, C. ; Wang, Y. ; Watanabe, Y. ; Wells, C. ; Wilming, L. G. ; Wynshaw-Boris, A. ; Yanagisawa, M. ; Yang, I. ; Yang, L. ; Yuan, Z. ; Zavolan, M. ; Zhu, Y. ; Zimmer, A. ; Carninci, P. ; Hayatsu, N. ; Hirozane-Kishikawa, T. ; Konno, H. ; Nakamura, M. ; Sakazume, N. ; Sato, K. ; Shiraki, T. ; Waki, K. ; Kawai, J. ; Aizawa, K. ; Arakawa, T. ; Fukuda, S. ; Hara, A. ; Hashizume, W. ; Imotani, K. ; Ishii, Y. ; Itoh, M. ; Kagawa, I. ; Miyazaki, A. ; Sakai, K. ; Sasaki, D. ; Shibata, K. ; Shinagawa, A. ; Yasunishi, A. ; Yoshino, M. ; Waterston, R. ; Lander, E. S. ; Rogers, J. ; Birney, E. ; Hayashizaki, Y. / Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. In: Nature. 2002 ; Vol. 420, No. 6915. pp. 563-573.
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abstract = "Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1{\%} of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41{\%} of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79{\%} of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.",
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TY - JOUR

T1 - Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

AU - Okazaki, Y.

AU - Furuno, M.

AU - Kasukawa, T.

AU - Adachi, J.

AU - Bono, H.

AU - Kondo, S.

AU - Nikaido, I.

AU - Osato, N.

AU - Saito, R.

AU - Suzuki, H.

AU - Yamanaka, I.

AU - Kiyosawa, H.

AU - Yagi, K.

AU - Tomaru, Y.

AU - Hasegawa, Y.

AU - Nogami, A.

AU - Schönbach, C.

AU - Gojobori, T.

AU - Baldarelli, R.

AU - Hill, D. P.

AU - Bult, C.

AU - Hume, D. A.

AU - Quackenbush, J.

AU - Schriml, L. M.

AU - Kanapin, A.

AU - Matsuda, H.

AU - Batalov, S.

AU - Beisel, Kirk

AU - Blake, J. A.

AU - Bradt, D.

AU - Brusic, V.

AU - Chothia, C.

AU - Corbani, L. E.

AU - Cousins, S.

AU - Dalla, E.

AU - Dragani, T. A.

AU - Fletcher, C. F.

AU - Forrest, A.

AU - Frazer, K. S.

AU - Gaasterland, T.

AU - Gariboldi, M.

AU - Gissi, C.

AU - Godzik, A.

AU - Gough, J.

AU - Grimmond, S.

AU - Gustincich, S.

AU - Hirokawa, N.

AU - Jackson, I. J.

AU - Jarvis, E. D.

AU - Kanai, A.

AU - Kawaji, H.

AU - Kawasawa, Y.

AU - Kedzierski, R. M.

AU - King, B. L.

AU - Konagaya, A.

AU - Kurochkin, I. V.

AU - Lee, Y.

AU - Lenhard, B.

AU - Lyons, P. A.

AU - Maglott, D. R.

AU - Maltais, L.

AU - Marchionni, L.

AU - McKenzie, L.

AU - Miki, H.

AU - Nagashima, T.

AU - Numata, K.

AU - Okido, T.

AU - Pavan, W. J.

AU - Pertea, G.

AU - Pesole, G.

AU - Petrovsky, N.

AU - Pillai, R.

AU - Pontius, J. U.

AU - Qi, D.

AU - Ramachandran, S.

AU - Ravasi, T.

AU - Reed, J. C.

AU - Reed, D. J.

AU - Reid, J.

AU - Ring, B. Z.

AU - Ringwald, M.

AU - Sandelin, A.

AU - Schneider, C.

AU - Semple, C. A M

AU - Setou, M.

AU - Shimada, K.

AU - Sultana, R.

AU - Takenaka, Y.

AU - Taylor, M. S.

AU - Teasdale, R. D.

AU - Tomita, M.

AU - Verardo, R.

AU - Wagner, L.

AU - Wahlestedt, C.

AU - Wang, Y.

AU - Watanabe, Y.

AU - Wells, C.

AU - Wilming, L. G.

AU - Wynshaw-Boris, A.

AU - Yanagisawa, M.

AU - Yang, I.

AU - Yang, L.

AU - Yuan, Z.

AU - Zavolan, M.

AU - Zhu, Y.

AU - Zimmer, A.

AU - Carninci, P.

AU - Hayatsu, N.

AU - Hirozane-Kishikawa, T.

AU - Konno, H.

AU - Nakamura, M.

AU - Sakazume, N.

AU - Sato, K.

AU - Shiraki, T.

AU - Waki, K.

AU - Kawai, J.

AU - Aizawa, K.

AU - Arakawa, T.

AU - Fukuda, S.

AU - Hara, A.

AU - Hashizume, W.

AU - Imotani, K.

AU - Ishii, Y.

AU - Itoh, M.

AU - Kagawa, I.

AU - Miyazaki, A.

AU - Sakai, K.

AU - Sasaki, D.

AU - Shibata, K.

AU - Shinagawa, A.

AU - Yasunishi, A.

AU - Yoshino, M.

AU - Waterston, R.

AU - Lander, E. S.

AU - Rogers, J.

AU - Birney, E.

AU - Hayashizaki, Y.

PY - 2002/12/5

Y1 - 2002/12/5

N2 - Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

AB - Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

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