Assessing sources of variability in microarray gene expression data

BioTechniques

Volumn 33, Issue 4, 2002, Pages 916-923

  Spruill, Susan E ^a   Lu, Jun ^a   Hardy, Sarah ^a   Weir, Bruce ^a  

^a POZEN Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA ACQUISITION; DATA MINING; DATABASE SYSTEMS; GENETIC ENGINEERING;

GENE EXPRESSION; MICROARRAY EXPERIMENTS;

GENES;

ARTICLE; DATA BASE; DNA MICROARRAY; GENE EXPRESSION; GENOME ANALYSIS; QUALITY CONTROL; REPRODUCIBILITY;

EID: 0036793353     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/02334mt05     Document Type: Article

References (27)

1. Alon, U., N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, and A.J. Levine. 1999. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 96:6745-6750.
2. Baldi, P. and A.D. Long. 2001. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17:509-519.
3. Becker, K.G. 2001. The sharing of cDNA microarray data. Nat. Rev. Neurosci. 2:438-440.
4. Brazma, A. and J. Vilo. 2000. Gene expression data analysis. FEBS Lett. 480:17-24.
5. Getz, G., E. Levine, and E. Domany. 2000. Coupled two-way clustering analysis of gene microarray data. Proc. Natl. Acad. Sci. USA 97:12079-12084.
6. Hilsenbeck, S.G., W.E. Friedrichs, R. Schiff, P. O'Connell, R.K. Hansen, C.K. Osborne, and S.A.W. Fuqua. 1999. Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J. Natl. Cancer Inst. 95:453-459.
7. Kaminski, N., J.D. Allard, J.F. Pittet, F. Zuo, M.J.D. Griffith, D. Morris, X. Huang, D. Sheppard, et al. 2000. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis. Proc. Natl. Acad. Sci. USA 97:1778-1783.
8. Kerr, M.K., C.A. Afshari, L. Bennett, P. Bushel, J. Martinez, N.J. Walker, and G.A. Churchill. 2002. Statistical analysis of a gene expression microarray experiment with replication. Statistica Sinica 12:203-217.
9. Kerr, M.K. and G.A. Churchill. 2001. Experimental design for gene expression microarrays. Biostatistics 2:183-201.
10. Kerr, M.K. and G.A. Churchill. 2001. Statistical design and the analysis of gene expression microarray data. Genet. Res. 77:123-128.
11. Kerr, M.K., M. Martin, and G.A. Churchill. 2001. Analysis of variance for gene expression microarray data. J. Comput. Bio. 7:819-837.
12. Kerr, M.K., E.H. Leiter, L. Picard, and G.A. Churchill. 2001. Analysis of a designed microarray experiment. Proceedings of the IEEE-Eurasip Nonlinear Signal and Image Processing Workshop. June 3-6, 2001.
13. Kim, S., E.R. Dougherty, M.L. Bittner, Y. Chen, K. Sivakumar, P. Meltzer, and J.M. Trent. 2000. General nonlinear framework for the analysis of gene interaction via multivariate expression arrays. J. Biomed. Opt. 5:411-424.
14. Lee, M.T., F.C. Kuo, G.A. Whitmore, and J. Sklar. 2000. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA 97:9834-9839.
15. Leung, Y.F., D.S.C. Lam, and C.P. Pang. 2001. The miracle of microarray data analysis. Genome Biol. 2:4021.1-4021.2.
16. Loos, A., C. Glanemann, L.B. Willis, X.M. O'Brien, P.A. Lessard, R. Gerstmeir, S. Guillouet, and A.J. Sinskey. 2001. Development and validation of corynebacterium DNA microarrays. Appl. Environ. Microbiol. 67:2310-2318.
17. Mirnics, K. 2001. Mircoarrays in brain research: the good, the bad, and the ugly. Nat. Rev. Neursci. 2:444-447.
18. Newton, M.A., C.M. Kendziorski, C.S. Richmond, F.R. Blattner, and K.W. Tsui. 2001. On differential variability of expression ratios: improving statistical inference about gene expression changes from mircoarray data. J. Comput. Biol. 8:37-52.
19. SAS Institute. SAS/STAT User's Guide, 4th edition. 1990. Version 6; volume 2. SAS Institute. Cary, NC.
20. Scherf, U., D.T. Ross, M. Waltham, L.H. Smith, J.K. Lee, L. Tanabe, K.W. Kohn, W.C. Reinhold, et al. 2000. A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 24:236-244.
21. Sherlock, G. 2000. Analysis of large-scale expression data. Curr. Opin. Immunol. 12:201-205.
22. Schuchhardt, J., D. Beule, A. Malik, E. Wolski, H. Eickhoff, H. Lehrach, and H. Herzel. 2000. Normalization strategies for cDNA microarrays. Nucleic Acids Res. 28:e47i-v.
23. Siedow, J.N. 2001. Making sense of microarrays. Genome Biol. 2:4003.1-4003.2.
24. Tamayo, P., D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E.S. Lander, and T.R. Golub. 1999. Interpreting patterns of gene expression with self-organizing maps: methods and applications to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA 96:2907-2912.
25. Wildsmith, S.E., G.E. Archer, A.J. Winkley, P.W. Lane, and P.J. Bugelski. 2001. Maximization of signal derived from cDNA microarrays. BioTechinques 30:202-208.
26. Wolfinger, R.D., G. Gibson, E.D. Wolfinger, L. Bennett, H. Hamadeh, P. Bushel, C. Afshari, and R.S. Paules. 2001. Assessing gene significance from cDNA microarray expression data via mixed models. J. Comput. Biol. 8:625-637.
27. Zhu, J. and M.Q. Zhang. 1999. Cluster, function, and promoter: analysis of yeast expression array. Pac. Symp. Biocomput. 5:476-487.