EVE (external variance estimation) increases statistical power for detecting differentially expressed genes

Plant Journal

Volumn 52, Issue 3, 2007, Pages 561-569

  Wille, Anja ^a   Gruissem, Wilhelm ^a   Bühlmann, Peter ^a   Hennig, Lars ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Affymetrix; Arabidopsis; Biological noise; Gene expression; Microarray; Statistical test

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; GENE EXPRESSION; OPTIMIZATION; STATISTICAL TESTS; STRESS ANALYSIS;

AFFYMETRIX; ARABIDOPSIS; BIOLOGICAL NOISE;

MICROARRAYS;

ALGORITHM; ARABIDOPSIS; ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY; STATISTICAL ANALYSIS;

ALGORITHMS; ARABIDOPSIS; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

ARABIDOPSIS;

EID: 35448944488     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2007.03227.x     Document Type: Article

References (34)

1. Altmann, T., Weigel, D. Nover, L. (2004) AtGenExpress - Ein multinational koordiniertes Programm zur Erforschung des Arabidopsis Transkriptoms. GenomXpress, 3, 13 14.
2. Benjamini, Y. Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. [B], 57, 289 300.
3. Benjamini, Y. Yekutieli, D. (2001) The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29, 1165 1188.
4. Brazma, A., Hingamp, P., Quackenbush, J. et al. (2001) Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat. Genet. 29, 365 371.
5. Brazma, A., Parkinson, H., Sarkans, U. et al. (2003) ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 68 71.
6. Breiman, L., Friedman, J.H., Olshen, R.A. Stone, C.J. (1984) Classification and Regression Trees. Pacific Grove, CA : Wadsworth.
7. Chubb, J.R., Trcek, T., Shenoy, S.M. Singer, R.H. (2006) Transcriptional pulsing of a developmental gene. Curr. Biol. 16, 1018 1025.
8. Craigon, D.J., James, N., Okyere, J., Higgins, J., Jotham, J. May, S. (2004) NASCarrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res. 32, D575 D577.
9. Cui, X. Churchill, G.A. (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 4, 210.1 210.10.
10. Efron, N., Tibshirani, R., Storey, J. Tusher, V.G. (2001) Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Assoc. 96, 1151 1160.
11. Hennig, L., Menges, M., Murray, J.A.H. Gruissem, W. (2003) Arabidopsis transcript profiling on Affymetrix genechip arrays. Plant Mol. Biol. 53, 457 465.
12. Huber, W., Heydebreck, A.V., Sultmann, H., Poustka, A. Vingron, M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18, S96 S104.
13. Ihaka, R. Gentleman, R. (1996) R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5, 299 314.
14. Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U. Speed, T.P. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249 264.
15. Jain, N., Thatte, J., Braciale, T., Ley, K., O'Connell, M. Lee, J.K. (2003) Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. Bioinformatics, 19, 1945 1951.
16. Kendziorski, C.M., Newton, M.A., Lan, H. Gould, M.N. (2003) On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Stat. Med. 22, 3899 3914.
17. Kim, R.D. Park, P.J. (2004) Improving identification of differentially expressed genes in microarray studies using information from public databases. Genome Biol. 5, R70.1 R70.10.
18. Liu, W.M., Mei, R., Di, X. et al. (2002) Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics, 18, 1593 1599.
19. Newman, J.R., Ghaemmaghami, S., Ihmels, J., Breslow, D.K., Noble, M., DeRisi, J.L. Weissman, J.S. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature, 441, 840 846.
20. Newton, M.A., Kendziorski, C.M., Richmond, C.S., Blattner, F.R. Tsui, K.W. (2001) On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J. Comput. Biol. 8, 37 52.
21. Quackenbush, J. (2002) Microarray data normalization and transformation. Nat. Genet. 32 (Suppl. 496 501.
22. Redman, J.C., Haas, B.J., Tanimoto, G. Town, C.D. (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J. 38, 545 561.
23. Rocke, D.M. Durbin, B. (2001) A model for measurement error for gene expression arrays. J. Comput. Biol. 8, 557 569.
24. Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Scholkopf, B., Weigel, D. Lohmann, J.U. (2005) A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37, 501 506.
25. Smyth, G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, 1 26.
26. Smyth, G.K., Yang, Y.H. Speed, T. (2003) Statistical issues in cDNA microarray data analysis. Methods Mol. Biol. 224, 111 136.
27. Stoughton, R.B. (2005) Applications of DNA microarrays in biology. Annu. Rev. Biochem. 74, 53 82.
28. Therneau, T.M. Atkinson, E.J. (1997) An Introduction to Recursive Partioning Using the rpart Routines. Technical Report 61. Rochester, NY : Department of Health Science Research, Mayo Clinic.
29. Tusher, V.G., Tibshirani, R. Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA, 98, 5116 5121.
30. Vandepoele, K., Vlieghe, K., Florquin, K., Hennig, L., Beemster, G.T., Gruissem, W., Van de Peer, Y., Inze, D. De Veylder, L. (2005) Genome-wide identification of potential plant E2F target genes. Plant Physiol. 139, 316 328.
31. Wu, Z., Irizarry, R.A., Gentleman, R., Murillo, F.M. Spencer, F. (2004) A Model Based Background Adjustment for Oligonucleotide Expression Arrays. Technical Report. Baltimore, MD : John Hopkins University, Department of Biostatistics.
32. Zien, A., Fluck, J., Zimmer, R. Lengauer, T. (2003) Microarrays: how many do you need? J. Comput. Biol. 10, 653 667.
33. Zimmermann, P., Hennig, L. Gruissem, W. (2005) Gene-expression analysis and network discovery using Genevestigator. Trends Plant Sci. 10, 407 409.
34. Zimmermann, P., Schildknecht, B., Craigon, D. et al. (2006) MIAME/Plant - adding value to plant microarrray experiments. Plant Methods, 2, 1.1 1.3.