Normalization and analysis of cDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine

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

Volumn 101, Issue 5, 2004, Pages 1135-1140

  Fan, Jianqing ^a   Tam, Paul ^b   Vande Woude, George ^c   Ren, Yi ^b  

^a Princeton University   (United States)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

^c VAN ANDEL RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOKINE;

ARTICLE; BIOTECHNOLOGY; CELL DIVISION; CLINICAL PROTOCOL; CONTROLLED STUDY; DNA MICROARRAY; GENE; GENE EXPRESSION; GENE INDUCTION; GENETIC ANALYSIS; GROWTH RELATED GENE; HUMAN; HUMAN CELL; IMMUNORELATED GENE; MOLECULAR MECHANICS; NEUROBLASTOMA CELL; NUCLEOTIDE SEQUENCE; ONCOGENE; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; STATISTICS; TUMOR GROWTH; TUMOR METASTATIC GENE; UPREGULATION;

GENE EXPRESSION PROFILING; HUMANS; MACROPHAGE MIGRATION-INHIBITORY FACTORS; NEUROBLASTOMA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 0842321044     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0307557100     Document Type: Article

References (34)

1. Brown, P. O. & Botstein, D. (1999) Nat. Genet. 21, Suppl. 1, 33-37.
2. Lee, M. T., Kuo, F. C., Whitmore, G. A. & Sklar, J. (2000) Proc. Natl. Acad. Sci. USA 18, 9834-9839.
3. Dudoit, Y., Yang, Y. H., Callow, M. J. & Speed, T. P. (2002) Stat. Sinica 12, 111-139.
4. Tseng, G. C., Oh, M. K., Rohlin, L., Liao, J. C. & Wong, W. H. (2001) Nucleic Acids Res. 29, 2549-2557.
5. Kroll, T. C. & Wölfl, S. (2002) Nucleic Acids Res. 30, 1-6.
6. Huang, J., Kuo, H. C., Koroleva, I., Zhang, C. H. & Soares, M. B. (2003) Technical Report 321 (Department of Statistics, University of Iowa, Iowa City).
7. Kerr, J. K., Martin, M. & Churchill, G. A. (2000) J. Comput. Biol. 7, 819-837.
8. Zhang, H. P., Yu, C.-Y. & Singer, B. (2003) Proc. Natl. Acad. Sci. USA 100, 4168-4172.
9. Tusher, V. G., Tibshirani, R. & Chu, G. (2001) Proc. Natl. Acad. Sci. USA 98, 5116-5121.
10. Lönnstedt, I. & Speed, T. (2002) Stat. Sinica 12, 31-46.
11. Newton, M. A., Kendziorski, C. M., Richmond, C. S., Blanttner, F. R. & Tsui, K. W. (2001) J. Comput. Biol. 8, 37-52.
12. Tibshirani, R., Hastie, T., Narasimhan, B. & Chu, G. (2002) Proc. Natl. Acad. Sci. USA 99, 6567-6572.
13. Smyth, G. K., Yang, Y. H. & Speed, T. (2002) in Functional Genomics: Methods and Protocols, eds. Brownstein, M. J. B. & Khodursky, A. B. (Humana, Clifton, NJ), pp. 111-136.
14. Grolleau, A., Bowman, J., Pradet-Balade, B., Puravs, E., Hanash, S., Garcia-Sanz, J. A. & Beretta, L. (2002) J. Biol. Chem. 277, 22175-22184.
15. Maris, J. M. & Matthay, K. K. (1999) J. Clin. Oncol. 17, 2264-2279.
16. Mitchell, R. A. & Bucala, R. (2000) Semin. Cancer Biol. 10, 359-366.
17. Kamimura, A., Kamachi, M., Nishihira, J., Ogura, S., Isobe, H., Dosaka-Akita, H., Ogata, A., Shindoh, M., Ohbuchi, T. & Kawakami, Y. (2000) Cancer 89, 334-341.
18. Ren, Y., Tsui, H. T., Poon, R. T. P., Ng, I. O., Li, Z., Chen, Y., Jiang, G., Lau, C., Yu, W. C., Bacher, M. & Fan, S. T. (2003) Int. J. Cancer 107, 22-29.
19. Hastie, T. J. & Tibshirani, R. (1990) Generalized Additive Models (Chapman & Hall, London).
20. Fan, J. & Gijbels, I. (1996) Local Polynomial Modelling and Its Applications (Chapman & Hall, London).
21. Cleveland, W. S. (1979). J. Am. Stat. Assoc. 74, 829-836.
22. Fan, J. & Yao, Q. (1998) Biometrika 85, 645-660.
23. Reiner, A., Yekutieli, D. & Benjamini, Y. (2003) Bioinformatics 19, 368-375.
24. Benjamini, Y. & Hochberg, Y. (1995) J. R. Stat. Soc. B, 57, 289-300.
25. Herdegen, T. & Leah, J. D. (1998) Brain Res. Rev. 28, 370-490.
26. Kunemund, V., Jungalwala, F. B., Fischer, G., Chou, D. K., Keilhauer, G. & Schachner, M. (1988) J. Cell Biol. 106, 213-223.
27. Wu, L. C. (2002) Gene Exp. 10, 137-152.
28. Bossolasco, M., Lebel, M., Lemieux, N. & Mes-Masson, A. M. (1999) Mol. Carcinog. 26, 189-200.
29. Bourguignon, J., Borghi, H., Sesboue, R., Diarra-Mehrpour, M., Bernaudin, J. F., Metayer, J., Martin, J. P. & Thiberville, L. (1999) J. Histochem. Cytochem. 47, 1625-1632.
30. De Schrijver, E., Brusselmans, K., Heyns, W., Verhoeven, G. & Swinnen, J. V. (2003) Cancer Res. 63, 3799-3804.
31. Wong, J. M., Mafune, K., Yow, H., Rivers, E. N., Ravikumar, T. S., Steele, G. D., Jr. & Chen, L. B. (1993) Cancer Res. 53, 1916-1920.
32. Gross, S. D., Simerly, C., Schatten, G. & Anderson, R. A. (1997). J. Cell Sci. 110, 3083-3090.
33. Hagedorn, H. G., Tubel, J., Wiest, I., Schleicher, E. D. & Nerlich, A. G. (1998) Anticancer Res. 18, 201-207.
34. Krecicki, T., Zalesska-Krecicka, M., Jelen, M., Szkudlarek, T. & Horobiowska, M. (2001) Clin. Otolaryngol. 26, 469-472.