Predicting aberrant CpG island methylation

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

Volumn 100, Issue 21, 2003, Pages 12253-12258

  Feltus, F A ^a,e   Lee, E K ^a,b   Costello, J F ^c   Plass, C ^d   Vertino, P M ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Georgia Institute of Technology   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d OHIO STATE UNIVERSITY   (United States)

^e UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA (CYTOSINE 5) METHYLTRANSFERASE;

ARTICLE; CHROMOSOMAL LOCALIZATION; CPG ISLAND; DNA METHYLATION; GENE LOCUS; GENE OVEREXPRESSION; GENE SILENCING; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROMOTER REGION;

BASE SEQUENCE; CELL LINE; CPG ISLANDS; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA METHYLATION; DNA, NEOPLASM; GENE EXPRESSION; GENE SILENCING; GENES, TUMOR SUPPRESSOR; GENOME, HUMAN; HUMANS; NEOPLASMS; PROMOTER REGIONS (GENETICS);

EID: 0142059820     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.2037852100     Document Type: Article

References (50)

1. Bird, A. P. (1986) Nature 321, 209-213.
2. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001) Nature 409, 860-921.
3. Antequera, F., Boyes, J. & Bird, A. (1990) Cell 62, 503-514.
4. Baylin, S. B., Herman, J. G., Graff, J. R., Vertino, P. M. & Issa, J. P. (1998) Adv. Cancer Res. 72, 141-196.
5. Costello, J. F. & Plass, C. (2001) J. Med. Genet. 38, 285-303.
6. Jones, P. A. & Baylin, S. B. (2002) Nat. Rev. Genet. 3, 415-428.
7. Esteller, M., Corn, P. G., Baylin, S. B. & Herman, J. G. (2001) Cancer Res. 61, 3225-3229.
8. Costello, J. F., Fruhwald, M. C., Smiraglia, D. J., Rush, L. J., Robertson, G. P., Gao, X., Wright, F. A., Feramisco, J. D., Peltomaki, P., Lang, J. C., et al. (2000) Nat. Genet. 24, 132-138.
9. Clark, S. J. & Melki, J. (2002) Oncogene 21, 5380-5387.
10. Esteller, M., Fraga, M. F., Guo, M., Garcia-Foncillas, J., Hedenfalk, I., Godwin, A. K., Trojan, J., Vaurs-Barriere, C., Bignon, Y. J., Ramus, S., et al. (2001) Hum. Mol. Genet. 10, 3001-3007.
11. Myohanen, S. K., Baylin, S. B. & Herman, J. G. (1998) Cancer Res. 58, 591-593.
12. Yates, P. A., Burman, R. W., Mummaneni, P., Krussel, S. & Turker, M. S. (1999) J. Biol. Chem. 274, 36357-36361.
13. Graff, J. R., Herman, J. G., Myohanen, S., Baylin, S. B. & Vertino, P. M. (1997) J. Biol. Chem. 272, 22322-22329.
14. Millar. D. S., Paul, C. L., Molloy, P. L. & Clark, S. J. (2000) J. Biol. Chem. 275, 24893-24899.
15. Turker, M. S. (1999) Semin. Cancer Biol. 9, 329-337.
16. Robertson, K. D., Ait, S. A., Yokochi, T., Wade, P. A., Jones, P. L. & Wolffe, A. P. (2000) Nat. Genet. 25, 338-342.
17. Fuks, F., Burgers, W. A., Godin, N., Kasai, M. & Kouzarides, T. (2001) EMBO J. 20, 2536-2544.
18. Di Croce, L., Raker, V. A., Corsaro, M., Fazi, F., Fanelli, M., Faretta, M., Fuks, F., Lo, C. F., Kouzarides, T., Nervi, C., et al. (2002) Science 295, 1079-1082.
19. Vertino, P. M., Yen, R. W., Gao, J. & Baylin, S. B. (1996) Mol. Cell. Biol. 16, 4555-4565.
20. Plass, C., Weichenhan, D., Catanese, J., Costello, J. F., Yu, F., Yu, L., Smiraglia, D., Cavenee, W. K., Caligiuri, M. A., deJong, P. & Held, W. A. (1997) DNA Res. 4, 253-255.
21. Zardo, G., Tiirikainen, M. I., Hong, C., Misra, A., Feuerstein, B. G., Volik, S., Collins, C. C., Lamborn, K. R., Bollen, A., Pinkel, D., et al. (2002) Nat. Genet. 32, 453-458.
22. Lindsay, S. & Bird, A. P. (1987) Nature 327, 336-338.
23. Costello, J. F., Smiraglia, D. J. & Plass, C. (2002) Methods 27, 144-149.
24. Zhu, X., Deng, C., Kuick, R., Yung, R., Lamb, B., Neel, J. V., Richardson, B. & Hanash, S. (1999) Proc. Natl. Acad. Sci. USA 96, 8058-8063.
25. Gardiner-Garden, M. & Frommer, M. (1987) J. Mol. Biol. 196, 261-282.
26. Takai, D. & Jones, P. A. (2002) Proc. Natl. Acad. Sci. USA 99, 3740-3745.
27. Lee, E. K., Easton, E. L. & Johnson. E. L. (2001) Graphs Combinatorics, in press.
28. Breiman, L., Friedman, J. H., Olshen, R. A. & Stone, C. J. (1984) Classification and Regression Trees (Wadsworth and Brooks/Cole, New York).
29. Mathsoft (2001) S-Plus 6 User Manual (Mathsoft, Inc., Seattte).
30. Lee, E. K., Gallagher, R. J. & Patterson, D. (2003) INFORMS J. Comput. 15, 23-41.
31. Gallagher, R. J., Lee, E. K. & Patterson, D. (1997) Ann. Op. Res. 74, 65-88.
32. Kaufman, L. & Rousseeuw, P. J. (1990) Finding Groups in Data: An Introduction to Cluster Analysis (Wiley, New York).
33. Biniszkiewicz, D., Gribnau, J., Ramsahoye, B., Gaudet, F., Eggan, K., Humpherys, D., Mastrangelo, M. A., Jun, Z., Walter, J. & Jaenisch, R. (2002) Mol. Cell. Biol. 22, 2124-2135.
34. Miyoshi, N., Kuroiwa, Y., Kohda, T., Shitara, H., Yonekawa, H., Kawabe, T., Hasegawa, H., Barton, S. C., Surani, M. A., Kaneko-Ishino, T. & Ishino, F. (1998) Proc. Natl. Acad. Sci. USA 95, 1102-1107.
35. Jackson-Grusby, L., Beard, C., Possemato, R., Tudor, M., Fambrough, D., Csankovszki, G., Dausman, J., Lee, P., Wilson, C., Lander, E. & Jaenisch, R. (2001) Nat. Genet. 27, 31-39.
36. Raman, V., Martensen, S. A., Reisman, D., Evron, E., Odenwald, W. F., Jaffee, E., Marks, J. & Sukumar, S. (2000) Nature 405, 974-978.
37. Suh, E. R., Ha, C. S., Rankin, E. B., Toyota, M. & Traber, P. G. (2002) J. Biol. Chem. 277, 35795-35800.
38. Shiraishi, M., Sekiguchi, A., Oates, A. J., Terry, M. J. & Miyamoto, Y. (2002) Oncogene 21, 3659-3662.
39. Wu, J., Issa, J. P., Herman, J., Bassett, D. E. J., Nelkin, B. D. & Baylin, S. B. (1993) Proc. Natl. Acad. Sci. USA 90, 8891-8895.
40. Bakin, A. V. & Curran, T. (1999) Science 283, 387-390.
41. Eads, C. A., Nickel, A. E. & Laird, P. W. (2002) Cancer Res. 62, 1296-1299.
42. Eads, C. A., Danenberg, K. D., Kawakami, K., Saltz, L. B., Danenberg, P. V. & Laird, P. W. (1999) Cancer Res. 59, 2302-2306.
43. Bird, A. (2002) Genes Dev. 16, 6-21.
44. Ioshikhes, I. P. & Zhang, M. Q. (2000) Nat. Genet. 26, 61-63.
45. Zhang, M. Q. (2002) Nat. Rev. Genet. 3, 698-709.
46. Yoder, J. A., Walsh, C. P. & Bestor, T. H. (1997) Trends Genet. 13, 335-340.
47. Li, G., Tolstonog, G. V. & Traub, P. (2002) DNA Cell Biol. 21, 163-188.
48. Vertino, P. M. (1999) in Eukaryotic DNA Methyltransferases, eds. Cheng, X. & Blumenthal, R. M. (World Scientific, River Edge, NJ), pp. 341-372.
49. Smiraglia, D. J. & Plass, C. (2002) Oncogene 21, 5414-5426.
50. Yan, P. S., Chen, C. M., Shi, H., Rahmatpanah, F., Wei, S. H., Caldwell, C. W. & Huang, T. H. (2001) Cancer Res. 61, 8375-8380.