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

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

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

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

Department of Computer Science

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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.

Translated title of the contribution	Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
Original language	English
Article number	563-573
Journal	Nature
Volume	420 (6915)
Publication status	Published - 2002

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Other identifier: 1040025

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Okazaki, Y., Suzuki, H., Yanagisawa, M., Yang, I., Yang, L., Yuan, Z., Zavolan, M., Zhu, Y., Zimmer, A., Carninci, P., Hayatsu, N., Hirozane-Kishikawa, T., Yamanaka, I., Konno, H., Nakamura, M., Sakazume, N., Sato, K., Shiraki, T., Waki, K., ... Wynshaw-Boris, A. (2002). Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420 (6915), Article 563-573. http://www.cs.bris.ac.uk/Publications/pub_master.jsp?id=1040025

@article{4783be85ef134d4398208ff85c3802c2,

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

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.",

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

note = "Other identifier: 1040025",

year = "2002",

language = "English",

volume = "420 (6915)",

journal = "Nature",

issn = "1476-4687",

publisher = "Springer Nature",

}

Okazaki, Y, Suzuki, H, Yanagisawa, M, Yang, I, Yang, L, Yuan, Z, Zavolan, M, Zhu, Y, Zimmer, A, Carninci, P, Hayatsu, N, Hirozane-Kishikawa, T, Yamanaka, I, Konno, H, Nakamura, M, Sakazume, N, Sato, K, Shiraki, T, Waki, K, Kawai, J, Aizawa, K, Arakawa, T, Fukuda, S, Kiyosawa, H, Hara, A, Hashizume, W, Imotani, K, Ishii, Y, Yagi, K, Tomaru, Y, Hasegawa, Y, Nogami, A, Schonbach, C, Gojobori, T, Baldarelli, R, Furuno, M, Hill, DP, Bult, C, Hume, DA, Quackenbush, J, Schriml, LM, Kanapin, A, Matsuda, H, Batalov, S, Beisel, KW, Blake, JA, Kasukawa, T, Bradt, D, Brusic, V, Chothia, C, Corbani, LE, Cousins, S, Dalla, E, Dragani, TA, Fletcher, CF, Forrest, A, Frazer, KS, Adachi, J, Gaasterland, T, Gariboldi, M, Gissi, C, Godzik, A, Gough, J, Grimmond, S, Gustincich, S, Hirokawa, N, Jackson, IJ, Jarvis, ED, Bono, H, Kanai, A, Kawaji, H, Kawasawa, Y, Kedzierski, RM, King, BL, Konagaya, A, Kurochkin, IV, Lee, Y, Lenhard, B, Lyons, PA, Kondo, S, Maglott, DR, Maltais, L, Marchionni, L, McKenzie, L, Miki, H, Nagashima, T, Numata, K, Okido, T, Pavan, WJ, Pertea, G, Nikaido, I, Pesole, G, Petrovsky, N, Pillai, R, Pontius, JU, Qi, D, Ramachandran, S, Ravasi, T, Reed, JC, Reed, DJ, Reid, J, Osato, N, Ring, BZ, Ringwald, M, Sandelin, A, Schneider, C, Semple, CA, Setou, M, Shimada, K, Sultana, R, Takenaka, Y, Taylor, MS, Saito, R, Teasdale, RD, Tomita, M, Verardo, R, Wagner, L, Wahlestedt, C, Wang, Y, Watanabe, Y, Wells, C, Wilming, LG & Wynshaw-Boris, A 2002, 'Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs', Nature, vol. 420 (6915), 563-573. <http://www.cs.bris.ac.uk/Publications/pub_master.jsp?id=1040025>

TY - JOUR

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

AU - Okazaki, Y.

AU - Suzuki, H.

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 - Yamanaka, I.

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 - Kiyosawa, H.

AU - Hara, A.

AU - Hashizume, W.

AU - Imotani, K.

AU - Ishii, Y.

AU - Yagi, K.

AU - Tomaru, Y.

AU - Hasegawa, Y.

AU - Nogami, A.

AU - Schonbach, C.

AU - Gojobori, T.

AU - Baldarelli, R.

AU - Furuno, M.

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, K. W.

AU - Blake, J. A.

AU - Kasukawa, T.

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 - Adachi, J.

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 - Bono, H.

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 - Kondo, S.

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 - Nikaido, I.

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 - Osato, N.

AU - Ring, B. Z.

AU - Ringwald, M.

AU - Sandelin, A.

AU - Schneider, C.

AU - Semple, C. A.

AU - Setou, M.

AU - Shimada, K.

AU - Sultana, R.

AU - Takenaka, Y.

AU - Taylor, M. S.

AU - Saito, R.

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.

N1 - Other identifier: 1040025

PY - 2002

Y1 - 2002

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.

M3 - Article (Academic Journal)

SN - 1476-4687

VL - 420 (6915)

JO - Nature

JF - Nature

M1 - 563-573

ER -

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

Abstract

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