Complete sequencing and characterization of 21,243 full-length human cDNAs

Nature Genetics

Volumn 36, Issue 1, 2004, Pages 40-45

  Ota, Toshio ^a,b   Suzuki, Yutaka ^c   Nishikawa, Tetsuo ^a,d   Otsuki, Tetsuji ^a   Sugiyama, Tomoyasu ^a   Irie, Ryotaro ^a   Wakamatsu, Ai ^a   Hayashi, Koji ^a   Sato, Hiroyuki ^a   Nagai, Keiichi ^a   Kimura, Kouichi ^d   Makita, Hiroshi ^d   Sekine, Mitsuo ^e   Obayashi, Masaya ^b   Nishi, Tatsunari ^b   Shibahara, Toshikazu ^c,f   Tanaka, Toshihiro ^c   Ishii, Shizuko ^a   Yamamoto, Jun ichi ^a   Saito, Kaoru ^a   Kawai, Yuri ^a   Isono, Yuko ^a   Nakamura, Yoshitaka ^a   Nagahari, Kenji ^a   Murakami, Katsuhiko ^d   Yasuda, Tomohiro ^d   Iwayanagi, Takao ^d   Wagatsuma, Masako ^d   Shiratori, Akiko ^d   Sudo, Hiroaki ^d   Hosoiri, Takehiko ^d   Kaku, Yoshiko ^d   Kodaira, Hiroyo ^d   Kondo, Hiroshi ^d   Sugawara, Masanori ^d   Takahashi, Makiko ^d   Kanda, Katsuhiro ^d   Yokoi, Takahide ^d   Furuya, Takako ^d   Kikkawa, Emiko ^d   Omura, Yuhi ^d   Abe, Kumi ^d   Kamihara, Kumiko ^d   Katsuta, Naoko ^d   Sato, Kazuomi ^d   Tanikawa, Machiko ^d   Yamazaki, Makoto ^d   Ninomiya, Ken ^d   Ishibashi, Tadashi ^d   Yamashita, Hiromichi ^d   Murakawa, Katsuji ^d   Fujimori, Kiyoshi ^d   Tanai, Hiroyuki ^d   Kimata, Manabu ^d   Watanabe, Motoji ^d   Hiraoka, Susumu ^d   Chiba, Yoshiyuki ^d   Ishida, Shinichi ^d   Ono, Yukio ^d   Takiguchi, Sumiyo ^d   Watanabe, Susumu ^d   Yosida, Makoto ^d   Hotuta, Tomoko ^d   Kusano, Junko ^d   Kanehori, Keiichi ^d   Takahashi Fujii, Asako ^g   Hara, Hiroto ^g   Tanase, Tomo o ^g   Nomura, Yoshiko ^g   Togiya, Sakae ^g   Komai, Fukuyo ^g   Hara, Reiko ^g   Takeuchi, Kazuha ^g   Arita, Miho ^g   Imose, Nobuyuki ^g   Musashino, Kaoru ^g   Yuuki, Hisatsugu ^g   Oshima, Atsushi ^g   Sasaki, Naokazu ^h   Aotsuka, Satoshi ^h   Yoshikawa, Yoko ^h   Matsunawa, Hiroshi ^h   Ichihara, Tatsuo ^h   Shiohata, Namiko ^h   Sano, Sanae ^h   Moriya, Shogo ^h   Momiyama, Hiroko ^h   Satoh, Noriko ^h   Takami, Sachiko ^h   Terashima, Yuko ^h   Suzuki, Osamu ^h   Nakagawa, Satoshi ^b   Senoh, Akihiro ^b   Mizoguchi, Hiroshi ^b   Goto, Yoshihiro ^f   Shimizu, Fumio ^f   Wakebe, Hirokazu ^f   Hishigaki, Haretsugu ^f   Watanabe, Takeshi ^f   Sugiyama, Akio ⁱ   Takemoto, Makoto ⁱ   Kawakami, Bunsei ⁱ   Yamazaki, Masaaki ^j   Watanabe, Koji ^j   Kumagai, Ayako ^j   Itakura, Shoko ^j   Fukuzumi, Yasuhito ^j   Fujimori, Yoshifumi ^j   Komiyama, Megumi ^j   Tashiro, Hiroyuki ^j   Tanigami, Akira ^f   Fujiwara, Tsutomu ^f   Ono, Toshihide ^f   Yamada, Katsue ^f   Fujii, Yuka ^f   Ozaki, Kouichi ^f   Hirao, Maasa ^f   Ohmori, Yoshihiro ^c,f   Kawabata, Ayako ^b   Hikiji, Takeshi ^b   Kobatake, Naoko ^b   Inagaki, Hiromi ^b   Ikema, Yasuko ^b   Okamoto, Sachiko ^b   Okitani, Rie ^b   Kawakami, Takuma ^c,f   Noguchi, Saori ^c   Itoh, Tomoko ^c   Shigeta, Keiko ^c   Senba, Tadashi ^c   Matsumura, Kyoka ^c   Nakajima, Yoshie ^c   Mizuno, Takae ^c   Morinaga, Misato ^c   Sasaki, Masahide ^c   Togashi, Takushi ^c   Oyama, Masaaki ^c   Hata, Hiroko ^c   Watanabe, Manabu ^c   Komatsu, Takami ^c   Mizushima Sugano, Junko ^c   Satoh, Tadashi ^c,d   Shirai, Yuko ^c   Takahashi, Yukiko ^c   Nakagawa, Kiyomi ^c   Okumura, Koji ^k   Nagase, Takahiro ^l   Nomura, Nobuo ^l,m   Kikuchi, Hisashi ^e   Masuho, Yasuhiko ^a   Yamashita, Riu ^c   Nakai, Kenta ^c   Yada, Tetsushi ^c   Nakamura, Yusuke ^c   Ohara, Osamu ^l   Isogai, Takao ^a   Sugano, Sumio ^c,m   more..

^a Helix Research Institute   (Japan)

^b KYOWA HAKKO KOGYO CO LTD   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d HITACHI LTD   (Japan)

^e NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

^f OTSUKA PHARMACEUTICAL CO LTD   (Japan)

^g TAKARA SHUZO CO LTD   (Japan)

^h Nisshinbo Industries Incorporated   (Japan)

ⁱ Toyobo Gene Analysis   (Japan)

^j Fujiya Co Ltd   (Japan)

^k Aisin Cosmos R and D Co   (Japan)

^l KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^m NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; DNA LIBRARY; DNA SEQUENCE; DNA SPLICING; DNA TRANSCRIPTION; GENETIC CODE; GENOMICS; HUMAN; MATHEMATICAL ANALYSIS; MOLECULAR CLONING; OPEN READING FRAME; PRIORITY JOURNAL;

CHROMOSOMES, HUMAN, 21-22 AND Y; CHROMOSOMES, HUMAN, PAIR 20; COMPUTATIONAL BIOLOGY; DNA, COMPLEMENTARY; HUMANS; OPEN READING FRAMES; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA;

EID: 9144252038     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1285     Document Type: Article

References (29)

1. Hattori, M. et al. The DNA sequence of human chromosome 21. Nature 405, 311-319 (2000).
2. Dunham, I. et al. The DNA sequence of human chromosome 22. Nature 402, 489-495 (1999).
3. Deloukas, P. et al. The DNA sequence and comparative analysis of human chromosome 20. Nature 414, 865-871 (2001).
4. Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
5. Venter, J.C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001)
6. Pruitt, K.D. & Maglott, D.R RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29, 137-140 (2001).
7. Boguski, M.S. The turning point in genome research. Trends Biochem. Sci. 20, 295-296 (1995).
8. Maruyama, K. & Sugano, S. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138, 171-174 (1994).
9. Suzuki, Y., Yoshitomo, K., Maruyama, K., Suyama, A & Sugano, S. Construction and characterization of a full length-enriched and a 5′-end-enriched cDNA library. Gene 200, 149-156 (1997).
10. Nomura, N. et al. Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1. DNA Res. 1, 27-35 (1994).
11. Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
12. Giesecke, H., Obermaier, B., Domdey, H. & Neubert, W.J. Rapid sequencing of the Sendai virus 6.8 kb large (L) gene through primer walking with an automated DNA sequencer. J. Virol. Methods. 38, 47-60 (1992).
13. Ewing, B., Hillier, L., Wendl, M.C. & Green, P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175-185 (1998).
14. Hubbard, T. et al. The Ensembl genome database project. Nucleic Acids Res. 30, 38-41 (2002).
15. Fickett, J.W. Predictive methods using nucleotide sequences. Methods Biochem. Anal. 39, 231-245 (1998).
16. Huttenhofer, A. et al. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J. 20, 2943-2953 (2001)
17. Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296. 916-919 (2002).
18. Burset, M. & Guigo, R. Evaluation of gene structure prediction programs. Genomics 34, 353-367 (1996).
19. Rogic, S., Mackworth, A.K. & Ouellette, F.B. Evaluation of gene-finding programs on mammalian sequences. Genome Res. 11, 817-832 (2001).
20. Yudate, H.T. et al. HUNT: launch of a full-length cDNA database from the helix research institute. Nucleic Acids Res. 29, 185-188 (2001).
21. Hattori, A. et al. Characterization of long cDNA clones from human adult spleen DNA Res. 7, 1-11 (2001).
22. Bernardi, G. The isochore organization of the human genome and its evolutionary history - a review Gene. 135, 57-66 (1993).
23. The FANTOM consortium and The RIKEN Genome Exploration Research Group Phase I & II team. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563-573 (2002).
24. Wiemann, S. et al. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Genome Res. 11, 422-435 (2001).
25. Strausberg, R.L., Feingold, E.A., Klausner, R.D. & Collins, F.S. The mammalian gene collection. Science 286, 455-457 (1999).
26. Gavin, A.C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
27. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002).
28. Chance, M.R. et al. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 11, 723-738 (2002).
29. Suzuki, Y, et al. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep. 2, 388-393 (2001).