A system for enhancing genome-wide coexpression dynamics study

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

Volumn 101, Issue 44, 2004, Pages 15561-15566

  Li, Ker Chau ^a   Liu, Ching Ti ^a   Sun, Wei ^a   Yuan, Shinsheng ^a   Yu, Tianwei ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alzheimer's disease; Gene expression; Microarray; Protein complex; Saccharomyces cerevisiae

Indexed keywords

AMYLOID PRECURSOR PROTEIN; APOLIPOPROTEIN E; BETA SECRETASE; FUNGAL PROTEIN; PRESENILIN 1; PRESENILIN 2;

ARTICLE; CANCER CELL CULTURE; CENTROMERE; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA BASE; GENE CONTROL; GENE EXPRESSION PROFILING; GENETIC MARKER; HUMAN; HUMAN GENOME; NONHUMAN; ONLINE SYSTEM; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; YEAST;

ALZHEIMER DISEASE; BIOMETRY; CELL LINE, TUMOR; GENE EXPRESSION PROFILING; GENOME, FUNGAL; GENOME, HUMAN; HUMANS; MACROMOLECULAR SUBSTANCES; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 8144222791     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0402962101     Document Type: Article

References (48)

1. Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. (1998) Proc. Natl. Acad. Sci. USA 95, 14863-14868.
2. Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E. S. & Golub, T. R. (1999) Proc. Natl. Acad. Sci. USA 96, 2907-2912.
3. Alter, O., Brown, P. O. & Botstein, D. (2000) Proc. Natl. Acad. Sci. USA 97, 10101-10106.
4. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O. & Eisenberg, D. (1999) Nature 402, 83-86.
5. Zhou, X., Kao, M. C. & Wong, W. H. (2002) Proc. Natl. Acad. Sci. USA 99, 12783-12788.
6. Li, K.-C. (2002) Proc. Natl. Acad. Sci. USA 99, 16875-16880.
7. Li, K.-C. & Yuan, S. (2004) Pharmacogenomics J. 4, 127-135.
8. Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C. R., Spellman, P., Iyer, V., Jeffrey, S. S., Van de Rijn, M., Waltham, M., et al. (2000) Nat. Genet. 24, 227-235.
9. Scherf, U., Ross, D. T., Waltham, M., Smith, L. H., Lee, J. K., Tanabe, L., Kohn, K. W., Reinhold, W. C., Myers, T. G., Andrews, M. D., et al. (2000) Nat. Genet. 24, 236-244.
10. Staunton, J. E., Slonim, D. K., Coller, H. A., Tamayo, P., Angelo, M. J., Park, J., Scherf, U., Lee, J. K., Reinhold, W. O., Weinstein, J. N., et al. (2001) Proc. Natl. Acad. Sci. USA 98, 10787-10792.
11. Spellman, T. P., Sherlock, G., Zhang, Q. M., Iyer, R. V., Anders, K., Eisen, B. M., Brown, O. P., Botstein, D. & Futcher, B. (1998) Mol. Biol. Cell 9, 3273-3297.
12. Brem, R., Yvert, G., Clinton, R. & Kruglyak, L. (2002) Science 296, 752-755.
13. Nika, J., Rippel, S. & Hannig, E. M. (2001) J. Biol. Chem. 276, 1051-1056.
14. Ramirez, C. V., Vilela, C., Berthelot, K. & McCarthy, J. E. (2002) J. Mol. Biol. 318, 951-962.
15. Ptushkina, M., von der Haar, T., Vasilescu, S., Frank, R., Birkenhäger, R. & McCarthy, E. G. J. (1998) EMBO J. 17, 4798-4808.
16. Das, S. & Maitra, U. (2001) Prog. Nucleic Acid Res. Mol. Biol. 70, 207-231.
17. Senapin, S., Clark-Walker, G. D., Chen, X. J., Seraphin, B. & Daugeron, M. C. (2003) Nucleic Acids Res. 31, 2524-2533.
18. Lieb, J. D., Liu, X., Botstein, D. & Brown, P. O. (2001) Nat. Genet. 28, 327-334, and erratum (2001) 29, 100.
19. Kilmartin, J. V. (2003) J. Cell Biol. 162, 1211-1221.
20. van Hemert, M. J., Deelder, A. M., Molenaar, C., Steensma, H. Y. & van Heusden, G. P. (2003) J. Biol. Chem. 278, 15049-15055.
21. Usui, T., Maekawa, H., Pereira, G. & Schiebel, E. (2003) EMBO J. 22, 4779-4793.
22. Euskirchen, G. M. (2002) Eukaryot. Cell 1, 229-240.
23. Saparbaev, M., Prakash, L. & Prakash, S. (1996) Genetics 142, 727-736.
24. Wendland, B., Steece, K. E. & Emr, S. D. (1999) EMBO J. 18, 4383-4393.
25. Lee, D., Kim, J. W., Seo, T., Hwang, S. G., Choi, E. J. & Choe, J. (2002) J. Biol. Chem. 277, 22330-22337.
26. Cao, X. & Südhof, T. C. (2001) Science 293, 115-120, and erratum (2001) 293, 1436.
27. Thomas, E. A., Laws, S. M., Sutcliffe, J. G., Harper, C., Dean, B., McClean, C., Masters, C., Lautenschlager, N., Gandy, S. E. & Martins, R. N. (2003) Biol. Psychiatry 54, 136-141.
28. Rodriguez, R. N. (1982) in Encyclopedia of Statistical Sciences, eds. Kotz, S. & Johnson, N. L. (Wiley, New York), Vol 2, pp. 193-204.
29. Hubert, P. (1985) Ann. Stat. 13, 435-526.
30. He, H., von der Haar, T., Singh, C. R., Ii, M., Li, B., Hinnebusch, A. G., McCarthy, J. E. & Asano, K. (2003) Mol. Cell. Biol. 23, 5431-5445.
31. Selkoe, D. J. (2001) Physiol. Rev. 81, 741-766.
32. Komano, H., Shiraishi, H., Kawamura, Y., Sai, X., Suzuki, R., Serneels, L., Kawaichi, M., Kitamura, T. & Yanagisawa, K. (2002) J. Biol. Chem. 277, 39627-39633.
33. Phiel, C. J., Wilson, C. A., Lee, V. M. & Klein, P. S. (2003) Nature 423, 435-439.
34. Axmark, D., Widenius, M. M., Cole, J. & DuBois, P. (1997) MySQL Reference Manual (MySQL, Uppsala).
35. Sklar, D. & Trachtenberg, A. (2003) PHP Cookbook (O'Reilly, Sebastopol, CA)
36. Press, H. W., Teukolsky, A. S., Vetterling, T. W. & Flannery, P. B. (2002) Numerical Recipes in C (Cambridge Univ. Press, New York), 2nd Ed.
37. Mouaikel, J., Bujnicki, J., Tazi, J. & Bordonne, R. (2003) Nucleic Acids Res. 31, 4899-4909.
38. Mizuta, K. & Warner, J. R. (1994) Mol. Cell. Biol. 14, 2493-2502.
39. Miyoshi, K., Miyakawa, T. & Mizuta, K. (2001) Nucleic Acids Res. 29, 3297-3303.
40. Galbiati, F., Volonte, D., Liu, J., Capozza, F., Frank, P. G., Zhu, L., Pestell, R. G. & Lisanti, M. P. (2001) Mol. Biol. Cell 12, 2229-2244.
41. Bacus, S. S., Yarden, Y., Oren, M., Chin, D. M., Lyass, L., Zelnick, C. R., Kazarov, A., Toyofuku, W., Gray-Bablin, J., Beerli, R. R., et al. (1996) Oncogene 12, 2535-2547.
42. Baron, B. W., Anastasi, J., Thirman, M. J., Furukawa, Y., Fears, S., Kim, D. C. Simone, F., Birkenbach, M., Montag, A., Sadhu, A., Zeleznik-Le, N. & McKeithan, T. W. (2002) Proc. Natl. Acad. Sci. USA 99, 2860-2865.
43. Kusam, S., Vasanwala, F. H. & Dent, A. L. (2004) Oncogene 23, 839-844.
44. Matt, T., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. (2004) Biochem. J. 381, 685-691.
45. Russo, C., Dolcini, V., Salis, S., Venezia, V., Zambrano, N., Russo, T. & Schettini, G., (2002) J. Biol. Chem. 277, 35282-35288.
46. Howard, L., Nelson, K. K., Maciewicz, R. A. & Blobel, C. P. (1999) J. Biol. Chem. 274, 31693-31699.
47. Asai, M., Hattori, C., Szabo, B., Sasagawa, N., Maruyama, K., Tanuma, S. & Ishiura, S. (2003) Biochem. Biophys. Res. Commun. 301, 231-235.
48. Stein, C. (1981) Ann. Stat. 9, 1135-1151.