A statistical framework for the design of microarray experiments and effective detection of differential gene expression

Bioinformatics

Volumn 20, Issue 16, 2004, Pages 2821-2828

  Zhang, Shu Dong ^a   Gant, Timothy W ^a  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ANALYSIS OF VARIANCE; ANALYTICAL ERROR; ARTICLE; CALCULATION; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN MICROARRAY; STATISTICAL ANALYSIS;

EID: 8844224836     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth336     Document Type: Article

References (26)

1. Baldi,P. and Hatfield,G.W. (2002) DNA Microarrays and Gene Expression. Cambridge University Press, Cambridge, UK.
2. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J.R. Statist. Soc. B, 57, 289-300.
3. Brownlee,K.A. (1965) Statistical Theory and Methodology in Science and Engineering. John Wiley and Sons, Inc., New York.
4. Callow,M.J., Dudoit,S., Gong,E.L., Speed,T.P. and Rubin, E.M. (2000) Microarray expression profiling identifies genes with altered expression in HDL-deficient mice. Genome Res., 10, 2022-2029.
5. Cheung,V.G., Morley,M., Aguilar,F., Massimi,A., Kucherlapati,R. and Childs,G. (1999) Making and reading microarrays. Nat. Genet., 21, 15-19.
6. Dobbin,K., Shih,J.H. and Simon,R. (2003) Statistical design for reverse dye microarrays. Bioinformatics, 19, 803-810.
7. Dobbin,K. and Simon,R. (2002) Comparison of microarray designs for class comparison and class discovery. Bioinformatics, 18, 1438-1445.
8. Dudoit,S., Yang,Y.H., Speed,T.P. and Callow,M.J. (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat. Sinica, 12, 111-139.
9. Efron,B., Tibshirani,R., Storey,J.D. and Tusher,V. (2001) Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Assoc., 96, 1151-1160.
10. Gant,T.W. and Zhang,S.-D. (2002) The bioinformatic challenge. In Life Sciences Review, BioArrays Conference, Cambridge, pp. 17-20.
11. Jin,W., Riley,R.M., Wolfinger,R.D., White,K.P., Passador-Gurgel,G. and Gibson,G. (2001) The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat. Genet., 29, 389-395.
12. Kerr,M.K., Afshari,C.A., Bennett,L., Bushel,P., Martinez,J., Walker,N.J. and Churchill,G.A. (2002) Statistical analysis of a gene expression microarray experiment with replication. Stat. Sinica, 12, 203-217.
13. Kerr,M.K., Martin,M. and Churchill,G.A. (2000) Analysis of variance for gene expression microarray data. J. Comput. Biol., 7, 819-837.
14. McShane,L.M., Shih,J.H. and Michalowska,A.M. (2003) Statistical issues in the design and analysis of gene expression microarray studies of animal models. J. MammaryGland Biol. Neoplasia 8, 359-374.
15. Pan,W, Lin,J. and Le,C. (2001) A Mixture model approach to detecting differentially expressed genes with microarray data. Research Report 2001-011. Division of Biostatistics, University of Minnesota.
16. Pan,W. (2003) On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression. Bioinformatics, 19, 1333-1340.
17. Pollack,J.R., Perou,C.M., Alizadeh,A.A., Eisen,M.B., Pergamenshikov,A., Williams,C.F., Jeffrey,S.S., Botstein,D. and Brown,P.O. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet., 23, 41-46.
18. Pounds,S. and Morris,S.W. (2003) Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics, 19, 1236-1242.
19. Quackenbush,J. (2002) Microarray data normalization and transformation. Nat. Genet., 32, 496-501.
20. Simon,R.M., Korn,E.L., McShane,L.M., Radmacher,M.D., Wright,G.W. and Zhao,Y. (2004) Design and Analysis of DNA Microarray Investigations. Gail,M., Krickberg,K., Samet,J., Tsiatis,A. and Wong,W. (eds), Statistics for Biology and Health (series) Springer.
21. Storey,J.D. and Tibshirani,R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci., USA, 100, 9440-9445.
22. Tseng,G.C., Oh,M.K., Rohlin,L., Liao,J.C. and Wong,W.H. (2001) Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res., 29, 2549-2557.
23. Tusher,V.G., Tibshirani,R. and Chu,G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci., USA, 98, 5116-5121.
24. Wernisch,L. (2002) Can replication save noisy microarray data? Comput. Funct. Genom., 3, 372-374.
25. Yang,Y.H., Dudoit,S., Luu,P., Lin,D.M., Peng,V., Ngai,J. and Speed,T.P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res., 30, e15.
26. Zhou,Y., Gwadry,F.G., Reinhold,W.C., Miller,L.D., Smith,L.H., Scherf,U., Liu,E.T., Kohn,K.W., Pommier,Y. and Weinstein, J.N. (2002) Transcriptional regulation of mitotic genes by camptothecin-induced DNA damage: microarray analysis of dose- and time-dependent effects. Cancer Res., 62, 1688-1695.