Significance analysis of time course microarray experiments

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

Volumn 102, Issue 36, 2005, Pages 12837-12842

  Storey, John D ^a   Xiao, Wenzhong ^b   Leek, Jeffrey T ^a   Tompkins, Ronald G ^c   Davis, Ronald W ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

Aging; Differential expression; Expression arrays; Q values; Time series

Indexed keywords

ADULT; AGE; AGED; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA MICROARRAY; DYNAMICS; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENOME ANALYSIS; HUMAN; HUMAN TISSUE; KIDNEY CORTEX; PRIORITY JOURNAL; SAMPLING; TECHNIQUE;

ADULT; AGED; AGED, 80 AND OVER; AGING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; INFLAMMATION; KIDNEY CORTEX; LIPOPOLYSACCHARIDES; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; TIME FACTORS;

EID: 24644519314     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0504609102     Document Type: Article

References (32)

1. Slonim, D. K. (2002) Nat. Genet. 32, 502-508.
2. Cui, X. & Churchill, G. A. (2003) Genome Biol. 4, 210.
3. Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. (1998) Proc. Natl Acad. Sci. USA 95, 14863-14868.
4. Zhu, G., Spellman, P. T., Volpe, T., Brown, P. O., Botstein, D., Davis, T. N. & Futcher, B. (2000) Nature 406, 90-94.
5. Alter, O., Brown, P. O. & Botstein, D. (2000) Proc. Natl. Acad. Sci. USA 97, 10101-10106.
6. Wakefield, J., Zhou, C. & Self, S. (2003) Bayesian Stat. 7, 721-732.
7. Bar-Joseph, Z., Gerber, G., Jaakkola, T. S., Gifford, D. K. & Simon, I. (2003) J. Comp. Bio. 10, 341-356.
8. Luan, Y. & Li, H. (2003) Bioinformatics 19, 474-482.
9. Bar-Joseph, Z., Gerber, G., Simon, I., Gifford, D. K. & Jaakkoia, T. S. (2003) Proc. Natl. Acad. Sci. USA 100, 10146-10151.
10. Diggle, P., Heagerty, P., Liang, K. Y. & Zeger, S. (2002) Analysis of Longitudinal Data (Oxford Univ. Press, Oxford), 2nd Ed.
11. Ramsay, J. O. & Silverman, B. W. (1997) Functional Data Analysis (Springer, Berlin).
12. Wang, Y. (1998) J. R. Stat. Soc. B 60, 159-174.
13. James, G. & Hastie, T. (2001) J. R. Stat. Soc. B 63, 533-550.
14. Rice, J. & Wu, C. (2001) Biometrics 57, 253-259.
15. Irizarry, R. A., Tankersley, C. G., Frank, R. & Flanders, S. E. (2001) Biometrics 57, 1228-1237.
16. James, G. & Sugar, C. (2003) J. Am. Stat. Assoc. 98, 397-408.
17. Calvano, S. E., Xiao, W., Richards, D. R., Felciano, R. M., Baker, H. V., Cho, R. J., Chen, R. O., Brownstein, B. H., Cobb, J. P., Tschoeke, S. K., et al. (2005) Nature, in press.
18. Rodwell, G. E. J., Sonu, R., Zahn, J. M., Lund, J., Wilhelmy, J., Wang, L., Xiao, W., Mindrinos, M., Crane, E., Segal, E., et al. (2004) PLoS Biol. 2, e427.
19. Hedenfalk, I., Duggan, D., Chen, Y. D., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O. P., et al. (2001) N. Engl. J. Med. 344, 539-548.
20. Tusher, V., Tibshirani, R. & Chu, C. (2001) Proc. Natl. Acad. Sci. USA 98, 5116-5121.
21. Higgins, J., Wang, L., Kambham, N., Montgomery, K., Maxon, V., Vogelmann, S., Lemley, K., Brown, P., Brooks, J. & van de Rijn, M. (2004) Mol. Biol. Cell 15, 649-656.
22. Li, C. & Wong, W. H. (2001) Proc. Natl. Acad. Sci. USA 98, 31-36.
23. Storey, J. D. & Tibshirani, R. (2003) Proc. Natl. Acad. Sci. USA 100, 9440-9445.
24. Efron, B. & Tibshirani, R. J. (1993) An Introduction to the Bootstrap (Chapman & Hall, Boca Raton, FL).
25. Storey, J. D. (2002) J. R. Stat. Soc. B 64, 479-498.
26. Hipfner, D. & Cohen, S. (2004) Nat. Rev. Mol. Cell Biol. 5, 805-816.
27. Yu, C., Yen, T., Lowell, C. & DeFranco, A. (2001) Curr. Biol. 11, 34-38.
28. Majeti, R., Xu, Z., Parslow, T., Olson, J., Daikh, D., Killeen, N. & Weiss, A. (2000) Cell 103, 1059-1070.
29. Mitchell, D., Pickering, M., Warren, J., Fossati-Jimack, L., Cortes-Hernandez, J., Cook, H., Botto, M. & Walport, M. (2002) J. Immunol. 168, 2538-2543.
30. Topham, P., Csizmadia, V., Soler, D., Hines, D., Gerard, C., Salant, D. & Hancock, W. (1999) J. Clin. Invest. 104, 1549-1557.
31. Gross, J., Johston, J., Mudri, S., Enselman, R., Dillon, S., Madden, K., Xu, W., Parrish-Novak, J., Foster, D., Lofton-Day, C., et al. (2000) Nature 404, 995-999.
32. Schilingmann, K., Weber, S., Peters, M., Niemann Nejsum, L., Vitzthum, H., Klingel, K., Kratz, M., Haddad, E., Ristoff, E., Dinour, D., et al. (2002) Nat. Genet. 31, 166-170.