CAGE Library

Shiraki, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100, 15776-15781 (2003).
Hwang B.J. et al., Genome annotation by high-throughput 5' RNA end determination. Proc. Natl. Acad. Sci. USA 101, 1650-1655 (2004),
Hashimoto, S. et al. 5'-end SAGE for the analysis of transcriptional start sites. Nat Biotechnol 22, 1146-1149 (2004).
Wei, C.L. et al. 5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. Proc Natl Acad Sci U S A 101, 11701-11706 (2004).
Zhang Z. and Dietrich F.S., Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nuc. Acids Res. 33, 2838-2851 (2005)

Harbers M and Carninci P., CAGE: A novel approach for rapid gene discovery and gene network identification in SAGE: Current Technologies and Applications, Horizon Bioscience 2005, ISBN: 1-904933-07-6
Harbers M and Carninci P., Tag-based approaches for transcriptome research and genome annotation. Nat Methods. 2,495-502 (2005)
Carninci P. Tagging mammalian transcription complexity. Trends Genet. 22:501-10. 2006.
Nakamura M, Carninci P, Tanpakushitsu Kakusan Koso. 49 (17 Suppl):2688-93 [Cap analysis gene expression: CAGE, article in Japanese. 2004.

Kodzius R. Matsumura Y, Kasukawa K, Shimokawa K, Fukuda S, Shiraki S. Nakamura M, Arakawa T, Sasaki D, Kawai J, Harbers M, Carninci P, Hayashizaki Y. Absolute Expression Values for Mouse Transcripts: Re-Annotation of the READ Expression Database by the Use of CAGE and EST Sequence Tags. Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags.FEBS Lett. 559: 22-6. 2004

Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P. The complexity of the mammalian transcriptome.J. Physiol. 575:321-32. 2006

Nilsson R, Bajic VB, Suzuki H, di Bernardo D, Bjorkegren J, Katayama S, Reid JF, Sweet MJ, Gariboldi M, Carninci P, Hayashizaki Y, Hume DA, Tegner J, Ravasi T. Transcriptional network dynamics in macrophage activation. Genomics. 88:133-42. 2006

Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A. Evolutionary turnover of mammalian transcription start sites. Genome Res. 16:713-22. 2006

Bajic VB, Tan SL, Christoffels A, Schonbach C, Lipovich L, Yang L, Hofmann O, Kruger A, Hide W, Kai C, Jawai J, Hume DA, Carninci P, Hayashizaki Y, Mice and men: Their Promoter properties, PLoS Genetics 2: e54. 2006

Seno S, Takenaka Y, Kai C, Kawai J, Carninci P, Hayashizaki Y, Matsuda H. A Method for Similarity Search of Genomic Positional Expression Using CAGE, PLoS Genetics 2: e44. 2006
Engstrom PG, Brozzi A, Luzi L, Sessa L, Lavorgna G, Tan SL, Yang L, Kunarso G, Ng ELC, Kai C, Kawai J, Carninci P, Hayashizak Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich L. Complex Loci in Human and Mouse Genomes, PLoS Genetics 2: e47.2006

Martin S. Taylor MS, Chikatoshi Kai C, Jun Kawai J, Carninci P, Hayashizaki Y, Semple CAM, Heterotachy in Mammalian Promoter Evolution, PLoS Genetics 2: e30. 2006

Hayashizaki Y and Carninci P. Genome Network and FANTOM 3 special issue of PLoS Genetics: Assessing the complexity of the transcriptome. PLoS Genetics 2: e63. 2006

Carninci P, Sandelin A, Lenhard B., Katayama S, Shimokawa S, Ponjavic J, Semple C, Taylor M, Engstrom P, Frith MC, Forrest ARR, Alkema W., Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y. Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data. Nat. Genetics, 38:626-35. 2006

Forrest AR, Taylor DF, Crowe ML, Chalk AM, Waddell NJ, Kolle G, Faulkner GJ, Kodzius R, Katayama S, Wells C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Grimmond SM. Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biol. 7:R5. 2006

Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M, Hayashizaki Y, Carninci P. CAGE: cap analysis of gene expression. Nat Methods. 3:211-22. 2006

Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, Kawai J, Carninci P, Hayashizaki Y. CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res. 34: D632-6. 2006

Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith MC, Ravasi T, Pang KC, Mattick JS, Hume DA, Lipovich L, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk A, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C. Antisense transcription in the mammalian transcriptome. Science 309:1564-6. 2005.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith M C, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic V B, Brenner S E, Batalov S, Forrest ARR, Zavolan M, Davis M J, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SPT, Kruger AF, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CAM, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegene E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y. The Transcriptional Landscape of the Mammalian Genome. Science. 309:1559-63. 2005

Metzker M.L., Emerging technologies in DNA sequencing. Genome Res. 15, 1767-1776 (2005),
Kling J., The search for a sequencing thoroughbred. Nature Biotechnology 23, 1333-1335 (2005)
Shendure J. et al., Advanced sequencing technologies: methods and goals. Nature Review Genetics 5, 335-344 (2004)