A novel algorithm for identification of activated cryptic 5′ splice sites

Journal of Biomolecular Structure and Dynamics

Volumn 29, Issue 5, 2012, Pages 1089-1099

  Tsai, Kun Nan ^a   Chen, Guang Wu ^b   Chen, Calvin Yu Chian ^c,d,e,f,g  

^a BIODIVERSITY RESEARCH CENTER   (Taiwan)

^b CHANG GUNG UNIVERSITY   (Taiwan)

^c CHINA MEDICAL UNIVERSITY   (Taiwan)

^d CHINA MEDICAL UNIVERSITY BEIGANG HOSPITAL   (Taiwan)

^e ASIA UNIVERSITY   (Taiwan)

^f HARVARD MEDICAL SCHOOL   (United States)

^g Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5' UNTRANSLATED REGION; ACCURACY; BINDING COMPETITION; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; GENE DELETION; GENE INSERTION; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROCESS DEVELOPMENT; REVIEW; RNA SEQUENCE; RNA SPLICING; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS;

EID: 84859323557     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/073911012010525033     Document Type: Article

References (59)

1. Baralle, D., and Baralle, M., 2005. J Med Genet, 42:737–748.
2. Krawczak, M., Reiss, J., and Cooper, D. N., 1992. Hum Genet, 90:41–54.
3. Nakai, K., and Sakamoto, H., 1994. Gene, 141:171–177.
4. Chen, X., Truong, T. T., Weaver, J., Bove, B. A., Cattie, K., Armstrong, B. A., Daly, M. B., and Godwin, A. K., 2006. Hum Mutat, 27:427–435.
5. Azevedo, J. E., Guimaraes, C. P., Lemos, M., Menezes, I., Coelho, T., and Sa-Miranda, C., 2001. Hum Genet, 109:616–622.
6. Roca, X., Sachidanandam, R., and Krainer, A. R., 2003. Nucleic Acids Research, 31:6321–6333.
7. Shapiro, M. B., and Senapathy, P., 1987. Nucleic Acids Research, 15:7155–7174.
8. Staden, R., 1984. Nucleic Acids Research, 12:505–519.
9. Salzberg, S. L., 1997. Bioinformatics, 13:365–376.
10. Buratti, E., Chivers, M., Královičová, J., Romano, M., Baralle, M., Krainer, A. R., and Vořechovský, I., 2007. Nucleic Acids Research, 35:4250–4263.
11. Roca, R. S. X., and Adrian, R., 2005. Krainer. RNA, 11:683–698.
12. Rogan, P. K., Faux, B. M., and Schneider, T. D., 1998. Hum Mutat, 12:153–171.
13. Nalla, V. K., and Rogan, P. K., 2005. Hum Mutat, 25:334–342.
14. Sahashi, K., Masuda, A., Matsuura, T., Shinmi, J., Zhang, Z., Takeshima, Y., Matsuo, M., Sobue, G., and Ohno, K., 2007. Nucleic Acids Research, 35:5995–6003.
15. Kapustin, Y., Chan, E., Sarkar, R., Wong, F., Vorechovsky, I., Winston, R. M., Tatusova, T., and Dibb, N. J., 2011. Nucleic Acids Research, 39:5837–5844.
16. Markham, N. R., and Zuker, M., 2005. Nucleic Acids Research, 33:W577–W581.
17. Puy, H., Gross, U., Deybach, J. C., Robreau, A. M., Frank, M., Nordmann, Y., and Doss, M., 1998. Hum Genet, 103:570–575.
18. Loo, J. C., Liu, L., Hao, A., Gao, L., Agatep, R., Shennan, M., Summers, A., Goldstein, A. M., Tucker, M. A., Deters, C., Fusaro, R., Blazer, K., Weitzel, J., Lassam, N., Lynch, H., and Hogg, D., 2003. Oncogene, 22:6387–6394.
19. Ishioka, C., Sato, T., Gamoh, M., Suzuki, T., Shibata, H., Kanamaru, R., Wakui, A., and Yamazaki, T., 1991. Biochem Biophys Res Commun, 177:901–906.
20. Gardella, R., Belletti, L., Zoppi, N., Marini, D., Barlati, S., and Colombi, M., 1996. Am J Hum Genet, 59:292–300.
21. Orii, K. E., Aoyama, T., Wakui, K., Fukushima, Y., Miyajima, H., Yamaguchi, S., Orii, T., Kondo, N., and Hashimoto, T., 1997. Hum Mol Genet, 6:1215–1224.
22. Coucke, P., Vits, L., Van Camp, G., Serville, F., Lyonnet, S., Kenwrick, S., Rosenthal, A., Wehnert, M., Munnich, A., and Willems, P. J., 1994. Hum Mol Genet, 3:671–673.
23. Tam, W., Gomez, M., Chadburn, A., Lee, J. W., Chan, W. C., and Knowles, D. M., 2006. Blood, 107:4090–4100.
24. Varley, J. M., Chapman, P., McGown, G., Thorncroft, M., White, G. R., Greaves, M. J., Scott, D., Spreadborough, A., Tricker, K. J., Birch, J. M., Evans, D. G., Reddel, R., Camplejohn, R. S., Burn, J., and Boyle, J. M., 1998. Oncogene, 16:3291–3298.
25. McGrory, J., and Cole, W. G., 1999. Clin Genet, 55:118–121.
26. Verlaan, D. J., Siegel, A. M., and Rouleau, G. A., 2002. Am J Hum Genet, 70:1564–1567.
27. Yip, K.-L., Chan, S.-Y., Ip, W.-K., and Lau, Y.-L., 2000. Hum Mutat, 15:385
28. Baumgartner, M. R., Almashanu, S., Suormala, T., Obie, C., Cole, R. N., Packman, S., Baumgartner, E. R., and Valle, D., 2001. J Clin Invest, 107:495–504.
29. Cherif-Zahar, B., Matassi, G., Raynal, V., Gane, P., Mempel, W., Perez, C., and Cartron, J. P., 1998. Blood, 92:639–646.
30. de Boer, M., Hartl, D., Wintergerst, U., Belohradsky, B. H., and Roos, D., 2005. Blood Cells Mol Dis, 35:365–369.
31. Wimmer, K., Roca, X., Beiglbock, H., Callens, T., Etzler, J., Rao, A. R., Krainer, A. R., Fonatsch, C., and Messiaen, L., 2007. Hum Mutat, 28:599–612.
32. Sevenet, N., Lellouch-Tubiana, A., Schofield, D., Hoang-Xuan, K., Gessler, M., Birnbaum, D., Jeanpierre, C., Jouvet, A., and Delattre, O., 1999. Hum Mol Genet, 8:2359–2368.
33. Anttonen, A. K., Mahjneh, I., Hamalainen, R. H., Lagier-Tourenne, C., Kopra, O., Waris, L., Anttonen, M., Joensuu, T., Kalimo, H., Paetau, A., Tranebjaerg, L., Chaigne, D., Koenig, M., Eeg-Olofsson, O., Udd, B., Somer, M., Somer, H., and Lehesjoki, A. E., 2005. Nat Genet, 37:1309–1311.
34. Alves, S., Mangas, M., Prata, M. J., Ribeiro, G., Lopes, L., Ribeiro, H., Pinto-Basto, J., Lima, M. R., and Lacerda, L., 2006. J Inherit Metab Dis, 29:743–754.
35. Treisman, R., Orkin, S. H., and Maniatis, T., 1983. Nature, 302:591–596.
36. Goldsmith, M. E., Humphries, R. K., Ley, T., Cline, A., Kantor, J. A., and Nienhuis, A. W., 1983. Proc Natl Acad Sci U S A, 80:2318–2322.
37. Celebi, J. T., Wanner, M., Ping, X. L., Zhang, H., and Peacocke, M., 2000. Hum Genet, 107:234–238.
38. Dale, D. C., Person, R. E., Bolyard, A. A., Aprikyan, A. G., Bos, C., Bonilla, M. A., Boxer, L. A., Kannourakis, G., Zeidler, C., Welte, K., Benson, K. F., and Horwitz, M., 2000. Blood, 96:2317–2322.
39. Van Kuilenburg, A. B., Meinsma, R., Beke, E., Bobba, B., Boffi, P., Enns, G. M., Witt, D. R., and Dobritzsch, D., 2005. Biol Chem, 386:319–324.
40. Ohno, K., Brengman, J. M., Felice, K. J., Cornblath, D. R., and Engel, A. G., 1999. Am J Hum Genet, 65:635–644.
41. Schwarze, U., Hata, R., McKusick, V. A., Shinkai, H., Hoyme, H. E., Pyeritz, R. E., and Byers, P. H., 2004. Am J Hum Genet, 74:917–930.
42. Symoens, S., Nuytinck, L., Legius, E., Malfait, F., Coucke, P. J., and De Paepe, A., 2004. J Med Genet, 41:e96
43. Atweh, G. F., Wong, C., Reed, R., Antonarakis, S. E., Zhu, D., Ghosh, P. K., Maniatis, T., Forget, B. G., and Kazazian, H. H., Jr. 1987. Blood, 70:147–151.
44. Vega, A., Campos, B., Bressac-De-Paillerets, B., Bond, P. M., Janin, N., Douglas, F. S., Domenech, M., Baena, M., Pericay, C., Alonso, C., Carracedo, A., Baiget, M., and Diez, O., 2001. Hum Mutat, 17:520–521.
45. Wadelius, C., Lagerkvist, A., Molin, A. K., Larsson, A., von Dobeln, U., and Pettersson, U., 1993. Genomics, 17:525–526.
46. Rugg, E. L., Rachet-Prehu, M. O., Rochat, A., Barrandon, Y., Goossens, M., Lane, E. B., and Hovnanian, A., 1999. Eur J Hum Genet, 7:293–300.
47. Kalatzis, V., Cherqui, S., Jean, G., Cordier, B., Cochat, P., Broyer, M., and Antignac, C., 2001. J Am Soc Nephrol, 12:2170–2174.
48. Tsujino, S., Tonin, P., Shanske, S., Nohria, V., Boustany, R. M., Lewis, D., Chen, Y. T., and DiMauro, S., 1994. Ann Neurol, 35:349–353.
49. Schwarze, U., Goldstein, J. A., and Byers, P. H., 1997. Am J Hum Genet, 61:1276–1286.
50. McNally, E. M., Ly, C. T., Rosenmann, H., Mitrani Rosenbaum, S., Jiang, W., Anderson, L. V., Soffer, D., and Argov, Z., 2000. Am J Med Genet, 91:305–312.
51. Lo Ten Foe, J. R., Rooimans, M. A., Bosnoyan-Collins, L., Alon, N., Wijker, M., Parker, L., Lightfoot, J., Carreau, M., Callen, D. F., Savoia, A., Cheng, N. C., van Berkel, C. G., Strunk, M. H., Gille, J. J., Pals, G., Kruyt, F. A., Pronk, J. C., Arwert, F., Buchwald, M., and Joenje, H., 1996. Nat Genet, 14:320–323.
52. Amir, R. E., Fang, P., Yu, Z., Glaze, D. G., Percy, A. K., Zoghbi, H. Y., Roa, B. B., and Van den Veyver, I. B., 2005. J Med Genet, 42:e15
53. Chen, C. Y. C., 2011. Plos One, 6:e15939
54. Sanderson, K., 2011. Nat Med, 17:1531
55. Chang, K. W., Tsai, T. Y., Chen, K. C., Yang, S. C., Huang, H. J., Chang, T. T., Sun, M. F., Chen, H. Y., Tsai, F. J., and Chen, C. Y., 2011. J Biomol Struct Dyn, 29:243–250.
56. Chen, C. Y., and Chen, C. Y. C., 2010. J Mol Graph Model, 29:21–31.
57. Chen, C. Y. C., 2010. J Taiwan Inst Chem E, 41:143–149.
58. Chen, Y. C., 2007. J Chin Chem Soc-Taip, 54:653–658.
59. Chen, C. Y., Chang, Y. H., Bau, D. T., Huang, H. J., Tsai, F. J., Tsai, C. H., and Chen, C. Y. C., 2009. Acta Pharmacol Sin, 30:1186–1194.