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The transcriptional landscape of the mammalian genome

Carninci, P. and Kasukawa, T. and Katayama, S. and Gough, J. and Frith, M. C. and Maeda, N. and Oyama, R. and Ravasi, T. and Lenhard, B. and Wells, C. and Kodzius, R. and Shimokawa, K. and Bajic, V. B. and Brenner, S. E. and Batalov, S. and Forrest, A. R. R. and Zavolan, M. and Davis, M. J. and Wilming, L. G. and Aidinis, V. and Allen, J. E. and Ambesi-Impiombato, A. and Apweiler, R. and Aturaliya, R. N. and Bailey, T. L. and Bansal, M. and Baxter, L. and Beisel, K. W. and Bersano, T. and Bono, H. and Chalk, A. M. and Chiu, K. P. and Choudhary, V. and Christoffels, A. and Clutterbuck, D. R. and Crowe, M. L. and Dalla, E. and Dalrymple, B. P. and de Bono, B. and Della Gatta, G. and di Bernardo, D. and Down, T. and Engstrom, P. and Fagiolini, M. and Faulkner, G. and Fletcher, C. F. and Fukushima, T. and Furuno, M. and Futaki, S. and Gariboldi, M. and Georgii-Hemming, P. and Gingeras, T. R. and Gojobori, T. and Green, R. E. and Gustincich, S. and Harbers, M. and Hayashi, Y. and Hensch, T. K. and Hirokawa, N. and Hill, D. and Huminiecki, L. and Iacono, M. and Ikeo, K. and Iwama, A. and Ishikawa, T. and Jakt, M. and Kanapin, A. and Katoh, M. and Kawasawa, Y. and Kelso, J. and Kitamura, H. and Kitano, H. and Kollias, G. and Krishnan, S. P. T. and Kruger, A. and Kummerfeld, S. K. and Kurochkin, I. V. and Lareau, L. F. and Lazarevic, D. and Lipovich, L. and Liu, J. and Liuni, S. and McWilliam, S. and Madan Babu, M. and Madera, M. and Marchionni, L. and Matsuda, H. and Matsuzawa, S. and Miki, H. and Mignone, F. and Miyake, S. and Morris, K. and Mottagui-Tabar, S. and Mulder, N. and Nakano, N. and Nakauchi, H. and Ng, P. and Nilsson, R. and Nishiguchi, S. and Nishikawa, S. and Nori, F. and Ohara, O. and Okazaki, Y. and Orlando, V. and Pang, K. C. and Pavan, W. J. and Pavesi, G. and Pesole, G. and Petrovsky, N. and Piazza, S. and Reed, J. and Reid, J. F. and Ring, B. Z. and Ringwald, M. and Rost, B. and Ruan, Y. and Salzberg, S. L. and Sandelin, A. and Schneider, C. and Schonbach, C. and Sekiguchi, K. and Semple, C. A. M. and Seno, S. and Sessa, L. and Sheng, Y. and Shibata, Y. and Shimada, H. and Shimada, K. and Silva, D. and Sinclair, B. and Sperling, S. and Stupka, E. and Sugiura, K. and Sultana, R. and Takenaka, Y. and Taki, K. and Tammoja, K. and Tan, S. L. and Tang, S. and Taylor, M. S. and Tegner, J. and Teichmann, S. A. and Ueda, H. R. and van Nimwegen, E. and Verardo, R. and Wei, C. L. and Yagi, K. and Yamanishi, H. and Zabarovsky, E. and Zhu, S. and Zimmer, A. and Hide, W. and Bult, C. and Grimmond, S. M. and Teasdale, R. D. and Liu, E. T. and Brusic, V. and Quackenbush, J. and Wahlestedt, C. and Mattick, J. S. and Hume, D. A. and Kai, C. and Sasaki, D. and Tomaru, Y. and Fukuda, S. and Kanamori-Katayama, M. and Suzuki, M. and Aoki, J. and Arakawa, T. and Iida, J. and Imamura, K. and Itoh, M. and Kato, T. and Kawaji, H. and Kawagashira, N. and Kawashima, T. and Kojima, M. and Kondo, S. and Konno, H. and Nakano, K. and Ninomiya, N. and Nishio, T. and Okada, M. and Plessy, C. and Shibata, K. and Shiraki, T. and Suzuki, S. and Tagami, M. and Waki, K. and Watahiki, A. and Okamura-Oho, Y. and Suzuki, H. and Kawai, J. and Hayashizaki, Y.. (2005) The transcriptional landscape of the mammalian genome. Science, Vol. 309, no. 5740. pp. 1559-1563.

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Official URL: http://edoc.unibas.ch/dok/A5259666

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Abstract

This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)
05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Zavolan)
UniBasel Contributors:van Nimwegen, Erik and Zavolan, Mihaela
Item Type:Article, refereed
Article Subtype:Research Article
Bibsysno:Link to catalogue
Publisher:American Association for the Advancement of Science
ISSN:0036-8075
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:14 Sep 2012 06:50
Deposited On:22 Mar 2012 13:30

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