Identification of differentially expressed genes with multivariate outlier analysis

Journal of Biopharmaceutical Statistics

Volumn 14, Issue 3, 2004, Pages 629-646

  Zhao, Hong Ya ^a   Yue, Patrick Y K ^a   Fang, Kai Tai ^a  

^a HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

Author keywords

CDNA Microarray; Gene expression data; Kurtosis coefficient (KC); Mahalanobis distance (MD); Mixture model; Multivariate outlier

Indexed keywords

ALGORITHM; ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; CADMIUM CHLORIDE; DATA INTERPRETATION, STATISTICAL; MALE; MICE; MICE, INBRED ICR; MICROCOMPUTERS; MODELS, STATISTICAL; MULTIVARIATE ANALYSIS; MUTAGENS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 4644299293     PISSN: 10543406     EISSN: None     Source Type: Journal    
DOI: 10.1081/BIP-200025654     Document Type: Article

References (36)

1. Baldi, P., Long, A. D. (2001). A Bayesian framework for the analysis of microarray expression data: regulized t-test and statistical inferences of gene changes. Bioin formatitcs 17:509-519.
2. Chen, Y., Dougherty, E. R., Bittner, M. L. (1997). Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Optics 2:364-374.
3. Choudhuri, S., McKim, J. M., Klaassen, C. D. (1993). Differential expression of the met-allothionein gene in liver and brain of mice and rats. Toxicol. Appl. Pharmacol. 119:1-10.
4. Cleveland, W. S. (1993). Visualizing Data. Murrary Hill, New Jersey: At&T Bell Laboratories.
5. DeRisi, J. L., Penland, L., Brown, P. O., Meltzer, P. S., Ray, M., Chen, Y., Su, Y. A., Trent, J. M. (1996). Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genetics 14:457-460.
6. Dudoit, S., Yang, Y. H., Callow, M. J., Speed, T. P. (2000). Statistical Methods for Identifying Differentially Expressed Genes in Replicated cDNA Microarray Data. Technical report 578, Statistics department, University of Cambridge, Berkeley.
7. Efron, B., Tibshirani, R., Goss, V., Chu, G. (2000). Microarrays and their use in a comparative experiment. http://www-stat.standford.edu/tibs/ research.html.
8. Efron, B., Tibshirani, R., Storey, J. D., Tusher, V. (2001). Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Assoc. 96:1151-1160.
9. Hampel, F. R., Rousseeuw, P. J., Stahel, W. A. (1986). Robust Statistics: The Approach Based on Influence Functions. New York: John Wiley.
10. Hayes, R. B. (1997). The carcinogenicity of metals in humans. Cancer Causes Control 8:371-385.
11. Hilsenbeck, S. G., Friedrichs, W. E., Schiff, R., O'Connell, P., Hansen, R. K., Os-borne, C. K., Fuqua, S. A. (1999). Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J. Natl. Cancer Inst. 91:400-401.
12. Huang, Q., Dunn, R. T., Jayadev, S., Disorbo, O., Pack, F. D., Farr, S. B., Stoll, R. E., Blanchard, K. T. (2001). Assessment of cisplation-induced nephrotoxicity by microarray technology. Toxicol Sci. 63:196-207.
13. Kazantzis, G., Blanks, R. G., Sullivan, K. R. (1992). Is cadmium a human carcinogen? IARC Sci. Publ. 118:435-446.
14. Kerr, M. K., Martin, M., Churchill, G. A. (2000). Analysis of variance for gene expression microarray data. J. Comput. Biology 7:819-837, http://www.stat. berkeley.edu/users.terry/zarray/Html/papersindex.html.
15. Kerr, M., Afshari, C., Bennett, L., Bushel, P., Martinez, J., Walker, N., Churchill, G. (2002). Statistical analysis of a gene expression microarray experiment with replication. Statistica Sinica 12:203-219.
16. Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H., Brown, E. L. (1996). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14:1675-1680.
17. Lonnstedt, I., Speed, T. (2002). Replicated microarray data. Statistica Sinica 12:31-46.
18. Newton, M. A., Kendziorski, C. M., Richmond, C. S., Blattner, F. R., Tsui, K. W. (2000). On differential variability of expression ratios: Improving statistical inference about gene expression change from microarray data. J. Comput. Biology 8:37-52.
19. Peña, D., Prieto, F. J. (2001). Multivariate outlier detection and robust covariance matrix estimation. Technometrics 43:286-300.
20. Rocke, D. M., Woodruff, D. L. (1996). Identification of outliers in multivariate data. J. Am. Stat. Assoc. 91:1047-1061.
21. Rousseeuw, P. J., Leroy, A. M. (1987). Robust Regression and Outlier Detection. New York: Wiley.
22. Rousseeuw, P. J., Van Driessen, K. (1999). A fast algorithm for the minimum covariance estimator. Technometrics 41:212-223.
23. Schena, M., Shalon, D., Davis, R. W., Brown, P. O. (1995). Quantitative monitoring of gene expression patterns with complementary DNA microarray. Science 270:467-470.
24. Schena, M., Shalon, D., Renu, H., Andrew, C., Patrick, O. B., Ronald, W. D. (1996). Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. 93:10614-10619.
25. Schwart, G. G., Reis, I. M. (2002). Is cadmium a cause of human pancreatic cancer? Cancer Epidemiol Biomarkers Prev. 9:139-45.
26. Teruyama, K., Abe, M., Nakano, T., Takahashi, S., Yamada, S., Sato, Y. (2001). Neurophilin-1 is a downstream target of transcription factor Ets-1 in human umbilical vein endothelial cells. Fed. Eur. Bio. Sci. 504:1-4.
27. Thomas, J. G., Olson, J. M., Tapscott, S. J., Zhao, L. P. (2001). An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles. Genome Res. 11:1227-1236.
28. Tusher, V. G., Tibshirani, R., Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98:5116-5121.
29. Waalkes, M. P., Perantoni, A. (1989). Apparent deficiency of metallothionein in the Wistar rat prostate. Toxicol. Appl. Pharmacol. 101:83-94.
30. Waalkes, M. P., Rehm, S. (1994). Cadmium and prostate cancer. J. Toxicol. Environ. Health 43:251-269.
31. Waalkes, M. P., Anver, M. R., Diwan, B. A. (1999a). Chronic toxic and carcinogenic effects of oral cadmium in the Noble (NBL/Cr) rat: induction of neoplastic and proliferative lesions of the adrenal, kidney, prostate, and testes. J. Toxicol. Environ. Health 58:199-214.
32. Waalkes, M. P., Anver, M. R., Diwan, B. A. (1999b). Carcinogenic effects of cadmium in the noble (NBL/Cr) rat: induction of pituitary, testicular, and injection site tumors and intraepithelial proliferative lesions of the dorsolateral prostate. Toxicol. Sci. 52:154-161.
33. West, M., Nevins, J. R., Marks, J. R., Balanchette, C., Zuzan, H. (2000a). DNA Microarray Data Analysis and Regression Modeling for Genetic Expression Profiling. Institute of Statistics and Decision Sciences Working Paper #15.
34. West, M. (2000b). Bayesian Regression Analysis in the "Largee p, Small n" Paradigm. Institute of Statistics and Decision Sciences Working Paper #22.
35. Yang, Y. H., Dudoit, S., Luu, P., Speed, T. P. (2000). Normalization for cDNA Microarray Data. Technical Report 589.
36. Zhao, B., Bowden, R. A., Stavchansky, S. A., Bowman, P. D. (2001). Human endothelial cell response to gram-negative lipopolysaccharide assessed with cDNA microarrays. AJP-Cell Physiol. 281:1587-1595.