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

Nature

Volumn 420, Issue 6915, 2002, Pages 563-573

  Okazaki, Y ^a,b   Furuno, M ^a   Kasukawa, T ^a,c   Adachi, J ^a   Bono, H ^a   Kondo, S ^a   Nikaido, I ^a,d   Osato, N ^a   Saito, R ^a,e   Suzuki, H ^a   Yamanaka, I ^a   Kiyosawa, H ^a,d   Yagi, K ^a   Tomaru, Y ^a,f   Hasegawa, Y ^a,d   Nogami, A ^a,d   Schonbach C ^a   Gojobori, T ^g   Baldarelli, R ^h   Hill, D P ^h   Bult, C ^h   Hume, D A ⁱ   Quackenbush, J ^j   Schriml, L M ^k   Kanapin, A ^l   Matsuda, H ^m   Batalov, S ⁿ   Beisel, K W ^o   Blake, J A ^h   Bradt, D ^h   Brusic, V ^p   Chothia, C ^q   Corbani, L E ^h   Cousins, S ^h   Dalla, E ^r   Dragani, T A ^s   Fletcher, C F ^n,t   Forrest, A ⁱ   Frazer, K S ^h,u   Gaasterland, T ^v   Gariboldi, M ^s   Gissi, C ^w   Godzik, A ^x   Gough, J ^q   Grimmond, S ⁱ   Gustincich, S ^y   Hirokawa, N ^z   Jackson, I J ^aa   Jarvis, E D ^ab   Kanai, A ^e   Kawaji, H ^c,m   Kawasawa, Y ^ac   Kedzierski, R M ^ac   King, B L ^h   Konagaya, A ^a   Kurochkin, I V ^a   Lee, Y ^j   Lenhard, B ^ad   Lyons, P A ^ae   Maglott, D R ^k   Maltais, L ^h   Marchionni, L ^r   McKenzie, L ^h   Miki, H ^z   Nagashima, T ^a   Numata, K ^e   Okido, T ^g   Pavan, W J ^af   Pertea, G ^j   Pesole, G ^w   Petrovsky, N ^ag   Pillai, R ^p   Pontius, J U ^k   Qi, D ^h   Ramachandran, S ^h   Ravasi, T ⁱ   Reed, J C ^x   Reed, D J ^h   Reid, J ^r   Ring, B Z ^ah   Ringwald, M ^h   Sandelin, A ^ad   Schneider, C ^r   Semple, C A M ^aa   Setou, M ^z   Shimada, K ^ai,aj   Sultana, R ^j   Takenaka, Y ^m   Taylor, M S ^aa   Teasdale, R D ⁱ   Tomita, M ^e   Verardo, R ^r   Wagner, L ^k   Wahlestedt, C ^ad   Wang, Y ^j   Watanabe, Y ^ai,aj   Wells, C ⁱ   Wilming, L G ^ak   Wynshaw Boris, A ^al   Yanagisawa, M ^ac   Yang, I ^j   Yang, L ^h   Yuan, Z ⁱ   Zavolan, M ^v   Zhu, Y ^h   Zimmer, A ^am   Carninci, P ^b   Hayatsu, N ^a   Hirozane Kishikawa, T ^a   Konno, H ^a   Nakamura, M ^a   Sakazume, N ^a   Sato, K ^f   Shiraki, T ^a   Waki, K ^a   Kawai, J ^a,b   Aizawa, K ^a   Arakawa, T ^a   Fukuda, S ^a   Hara, A ^a   Hashizume, W ^a   Imotani, K ^a   Ishii, Y ^a   Itoh, M ^b   Kagawa, I ^a   Miyazaki, A ^a   Sakai, K ^a   Sasaki, D ^a   Shibata, K ^b   Shinagawa, A ^a   Yasunishi, A ^a   Yoshino, M ^a   Waterston, R ^an   Lander, E S ^ao   Rogers, J ^ak   Birney, E ^l   Hayashizaki, Y ^a,b,d,f   more..

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b Japan Science and Technology Agency   (Japan)

^c NTT CORPORATION   (Japan)

^d YOKOHAMA CITY UNIVERSITY   (Japan)

^e KEIO UNIVERSITY   (Japan)

^f UNIVERSITY OF TSUKUBA   (Japan)

^g NATIONAL INSTITUTE OF GENETICS   (Japan)

^h JACKSON LABORATORY   (United States)

ⁱ UNIVERSITY OF QUEENSLAND   (Australia)

^j J CRAIG VENTER INSTITUTE   (United States)

^k NATIONAL INSTITUTES OF HEALTH   (United States)

^l EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^m OSAKA UNIVERSITY   (Japan)

ⁿ GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^o BOYS TOWN NATIONAL RESEARCH HOSPITAL   (United States)

^p Lab for Information Technology   (Singapore)

^q MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^r LNCIB   (Italy)

^s NATIONAL CANCER INSTITUTE   (Italy)

^t SCRIPPS RESEARCH INSTITUTE   (United States)

^u UNIVERSITY OF OREGON   (United States)

^v ROCKEFELLER UNIVERSITY   (United States)

^w UNIVERSITY OF MILAN   (Italy)

^x BURNHAM INSTITUTE   (United States)

^y HARVARD MEDICAL SCHOOL   (United States)

^z UNIVERSITY OF TOKYO   (Japan)

^aa UNIVERSITY OF EDINBURGH   (United Kingdom)

^ab DUKE UNIVERSITY MEDICAL CENTER   (United States)

^ac HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^ad KAROLINSKA INSTITUTE   (Sweden)

^ae ADDENBROOKE S HOSPITAL   (United Kingdom)

^af NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^ag CANBERRA HOSPITAL   (Australia)

^ah Applied Genomics Inc   (United States)

^ai Hirakata Ryoikuen   (Japan)

^aj HYOGO COLLEGE OF MEDICINE   (Japan)

^ak WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^al UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^am UNIVERSITY OF BONN   (Germany)

^an WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^ao WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

SPLICING;

DNA; GENES; PROTEINS; RNA;

CLONING;

COMPLEMENTARY DNA; MESSENGER RNA;

DNA; RODENT;

ALTERNATIVE RNA SPLICING; ARTICLE; DATA BASE; DNA SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOMICS; HUMAN GENOME; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS;

ALTERNATIVE SPLICING; AMINO ACID MOTIFS; ANIMALS; CHROMOSOMES, MAMMALIAN; CLONING, MOLECULAR; DATABASES, GENETIC; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENES; GENOMICS; HUMANS; MEMBRANE PROTEINS; MICE; PHYSICAL CHROMOSOME MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEOME; RNA, ANTISENSE; RNA, MESSENGER; RNA, UNTRANSLATED; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

MAMMALIA; RODENTIA;

EID: 0142104045     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature01266     Document Type: Article

References (53)

1. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
2. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
3. Hogenesch, J. B. et al. A comparison of the Celera and Ensembl predicted gene sets reveals little overlap in novel genes. Cell 106, 413-415 (2001).
4. Daly, M. J. Estimating the human gene count. Cell 109, 283-284 (2002).
5. Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919 (2002).
6. Harrison, P. M. et al. Molecular fossils in the human genome: Identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res. 12, 272-280 (2002).
7. Reik, W. & Walter, J. Genomic imprinting: Parental influence on the genome. Nature Rev. Genet. 2, 21-32 (2001).
8. Mattick, J. S. & Gagen, M. J. The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms. Mol. Biol. Evol. 18, 1611-1630 (2001).
9. Liang, F. et al. Gene index analysis of the human genome estimates approximately 120,000 genes. Nature Genet, 25, 239-240 (2000).
10. Saha, S. et al. Using the transcriptome to annotate the genome. Nature Biotechnol. 20, 508-512 (2002).
11. Camargo, A. A. et al. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome. Proc. Natl. Acad. Sci. USA 98, 12103-12108 (2001).
12. 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).
13. Strausberg, R. L., Feingold, E. A., Klausner, R. D. & Collins, E S. The mammalian gene collection. Science 286, 455-457 (1999).
14. Carninci, P. et al. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10, 1617-1630 (2000).
15. Carninci, P. et al. Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. Genomics 77, 79-90 (2001).
16. Konno, H. et al. Computer-based methods for the mouse full-length cDNA encyclopedia: Real-time sequence clustering for construction of a nonredundant cDNA library. Genome Res. 11, 281-289 (2001).
17. Pruitt, K. D. & Maglott, D. R. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29, 137-140 (2001).
18. Ashburner, M. et at. Gene ontology: tool for the unification of biology. Nature Genet. 25, 25-29 (2000).
19. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature (this issue).
20. Mural, R. J. et al. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296, 1661-1671 (2002).
21. Pilpel, Y., Sudarsanam, P. & Church, G. M. Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genet. 29, 153-159 (2001).
22. Smale, S. T. Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim. Biophys. Acta 1351, 73-88 (1997).
23. Brett, D., Pospisil, H., Valcarcel, J., Reich, J. & Bork, P. Alternative splicing and genome complexity. Nature Genet. 30, 29-30 (2002).
24. Florea, L., Hartzell, G., Zhang, Z., Rubin, G. M. & Miller, W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8, 967-974 (1998).
25. Modrek, B., Resch, A., Grasso, C. & Lee, C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 29, 2850-2859 (2001).
26. Pesole, G., Liuni, S. & D'Souza, M. PatSearch: A pattern marcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics 16, 439-450 (2000).
27. Ferrigno, O. et al. Transposable B2 SINE elements can provide mobile RNA polymerase II promoters. Nature Genet. 28, 77-81 (2001).
28. Sleutels, F., Zwart, R. & Barlow, D. P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810-813 (2002).
29. Apweiler, R. et al. InterPro - An integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16, 1145-1150 (2000).
30. Gough, J., Karplus, K., Hughey, R. & Chothia, C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol. 313, 903-919 (2001).
31. Kawaji, H. et al. Exploration of novel motifs derived from mouse cDNA sequences. Genome Res. 12, 367-378 (2002).
32. Murzin, A. G. Structural classification of proteins: New superfamilies. Curr. Opin. Struct. Biol. 6, 386-394 (1996).
33. Leipe, D. D., Wolf, Y. I., Koonin, E. V. & Aravind, L. Classification and evolution of P-loop GTPases and related ATPases. J. Mol. Biol. 317, 41-72 (2002).
34. Poirier, G. M. et al. Immune-associated nucleotide-1 (IAN-1) is a thymic selection marker and defines a novel gene family conserved in plants. J. Immunol. 163, 4960-4969 (1999).
35. Nielsen, H. & Krogh, A. Prediction of signal peptides and signal anchors by a hidden Markov model. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6, 122-130 (1998).
36. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305, 567-580 (2001).
37. The Gene Ontology Consortium Creating the gene ontology resource: Design and implementation. Genome Res. 11, 1425-1433 (2001).
38. Miki, H., Setou, M., Kaneshiro, K. & Hirokawa, N. All kinesin superfamily protein, KIF, genes in mouse and human. Proc. Natl. Acad. Sci. USA 98, 7004-7011 (2001).
39. Hirokawa, N. Kinesin and dynein superfamily proteins and the mechanism of organelle transport. Science 279, 519-526 (1998).
40. Weissman, A. M. Themes and variations on ubiquitylation. Nature Rev. Mol. Cell Biol. 2, 169-178 (2001).
41. Bairoch, A. The ENZYME database in 2000. Nucleic Acids Res. 28, 304-305 (2000).
42. Kanehisa, M., Goto, S., Kawashima, S. & Nakaya, A. The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002).
43. Carninci, P., Nakamura, M., Sato, K., Hayashizaki, Y. Brownstein, M. J. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques 33, 306-309 (2002).
44. Bang, M. L. et al. The complete gene sequence of titin, expression of an unusual approximately 700-kDa titin isoform, and its interaction with obscurin identify a novel Z-line to I-band linking system. Circ. Res. 89, 1065-1072 (2001).
45. Koenig, M. et al. Complete cloning of the Duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene in normal and affected individuals. Cell 50, 509-517 (1987).
46. Carninci, P., Shiraki, T., Mizuno, Y., Muramatsu, M. & Hayashizaki, Y. Extra-long first-strand cDNA synthesis. Biotechniques 32, 984-985 (2002).
47. Dreyer, S. D., Zheng, Q., Zabel, B., Winterpacht, A. & Lee, B. Isolation, characterization, and mapping of a zinc finger gene, ZFP95, containing both a SCAN box and an alternatively spliced KRAB A domain. Genomics 62, 119-122 (1999).
48. Schweighoffer, F. et al. Qualitative gene profiling: a novel tool in genomics and in pharmacogenomics that deciphers messenger RNA isoforms diversity. Pharmacogenomics 1, 187-197 (2000).
49. Shoemaker, D. D. et al. Experimental annotation of the human genome using microarray technology. Nature 409, 922-927 (2001).
50. Kent, W. J. BLAT - The BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
51. Smith, T. F. & Waterman, M. S. Identification of common molecular subsequences, J. Mol. Biol. 147, 195-197 (1981).
52. Pearson, W. R. Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11, 635-650 (1991).
53. Hill, D. P. et al. Program description: Strategies for biological annotation of mammalian systems: Implementing gene ontologies in mouse genome informatics, Genomics 74, 121-128 (2001).