A large-scale full-length cDNA analysis to explore the budding yeast transcriptome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 47, 2006, Pages 17846-17851

  Miura, Fumihito ^a,b   Kawaguchi, Noriko ^a,b   Sese, Jun ^a   Toyoda, Atsushi ^c   Hattori, Masahira ^a,c,d   Morishita, Shinichi ^a,b   Ito, Takashi ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^d KITASATO UNIVERSITY   (Japan)

Author keywords

Alternative splicing; Antisense transcript; Noncoding RNA; Transcription start site

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; ARTICLE; DNA DETERMINATION; DNA LIBRARY; DNA SEQUENCE; EUKARYOTIC CELL; GENETIC TRANSCRIPTION; INTRON; MEIOSIS; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION SITE;

5' UNTRANSLATED REGIONS; AMINO ACID SEQUENCE; DNA, COMPLEMENTARY; GENE LIBRARY; GENOME, FUNGAL; INTRONS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

EUKARYOTA; MAMMALIA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 33845223334     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0605645103     Document Type: Article

References (40)

1. Dolinski C, Botstein D (2005) Genome Res 15:1611-1619.
2. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, et al. (2002) Nature 418:387-391.
3. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, et al. (2004) Science 303:808-813.
4. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He, YD, et al. (2000) Cell 102:109-126.
5. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, et al. (2002) Science 298:799-804.
6. Ghaemmaghami S, Huh WK, Bower, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS (2003) Nature 425:737-741.
7. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK (2003) Nature 425:686-691.
8. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, et al. (2000) Nature 403:623-627.
9. Ito T, Chiba T, Ozawa R, Yosida M, Hattori M, Sakaki Y (2001) Proc Natl Acad Sci USA 98:4569-7574.
10. Gavin AC, Bosche, M. Krause R, Grandi P, Marzioch M, Bauer A, Shultz J, Rick JM, Michon AM, Cruciat CM, et al. (2002) Nature 415:141-147.
11. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, et al. (2002) Nature 415:180-183.
12. Cliften P, Sudarsanama P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M (2003) Science 301:71-76.
13. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Nature 423:241-254.
14. Olivas WM, Muhlrad D, Parker R (1997) Nucleic Acids Res 25:4619-4625.
15. Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M (2002) Nat Biotechnol 20:58-63.
16. Oshiro G, Wodicka LM, Washburn MP, Yates JR, III, Lockhart DJ, Winzeler EA (2002) Genome Res 12:1210-1220.
17. Velculescu VE, Zhang I, Zhou W, Vogelstein J, Basrai MA, Bassett, DE, Jr, Hieter P, Vogelstein B, Kinzler KW (1997) Cell 88:243-251.
18. Zhang Z, Dietrich FS (2005) Nucleic Acids Res 33:2838-2851.
19. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM (2006) Proc Natl Acad Sci USA 103:5320-5325.
20. Ohtake H, Ohtoko K, Ishimaru Y, Kato S (2004) DNA Res 11:305-309.
21. Kato S, Ohtoko K, Ohtake H, Kimura T (2005) DNA Res 12:53-62.
22. Oyama T, Yoshida M, Kamegai S, Kitano K, Miura F, Kawaguchi N, Onda M, Satou K, Ito T (2003) Genome Informatics 14:312-313.
23. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, et al. (2006) Nat Genet 38:626-635.
24. Vilela C, McCarthy JE (2003) Mol Microbiol 49:859-867.
25. Zhang Z, Dietrich FS (2005) Curr Genet 48:77-87.
26. He F, Li X, Spatrick P, Casillo R, Dong S, Jacobson A (2003) Mol Cell 12:1439-1452.
27. Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S (2002) Bioinformatics 18:298-305.
28. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, et al. (2006) Nature 440:637-643.
29. Walther TC, Brickner JH, Aguilar PS, Bernales S, Pantoja C, Walter P (2006) Nature 439:998-1003.
30. Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, Shemesh R, Novik A, Sorek R (2006) Genome Res 16:30-36.
31. Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, Thomson TM, Antonarakis SE, Guigo R (2006) Genome Res 16:37-44.
32. Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Regnault B, Devaux F, Namane A, Seraphin B, et al. (2005) Cell 121:725-737.
33. Davis CA, Ares M, Jr (2006) Proc Natl Acad Sci USA 103:3262-3267.
34. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al. (2005) Science 309:1564-1566.
35. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. (2005) Science 309:1559-1563.
36. Mattick JS, Makunin IV (2006) Hum Mol Genet 15:R17-R29.
37. Mendes Soares LM, Valcarcel J (2006) EMBO J 25:923-931.
38. Bickel KS, Morris DR (2006) Mol Cell 22:309-316.
39. Adams A, Gottschling DF, Kaiser CA, Stearns T (1997) Methods in Yeast Genetics (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY).
40. Iyer V, Struhl K (1996) Proc Natl Acad Sci USA 93:5208-5212.