Noise sampling method: An ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays

Bioinformatics

Volumn 19, Issue 11, 2003, Pages 1348-1359

  Draghici, Sorin ^a   Kulaeva, Olga ^a   Hoff, Bruce ^b   Petrov, Anton ^b   Shams, Soheil ^b   Tainsky, Michael A ^a  

^a WAYNE STATE UNIVERSITY   (United States)

^b BioDiscovery Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF VARIANCE; ARTICLE; CELL HYBRIDIZATION; CELL IMMORTALIZATION; CELL LINE; CONFIDENCE INTERVAL; DNA MICROARRAY; DOWN REGULATION; EMPIRICISM; FIBROBLAST; GENE CONTROL; GENE EXPRESSION; GENE MAPPING; GENETIC SELECTION; GENETIC VARIABILITY; HUMAN; INTERMETHOD COMPARISON; LABORATORY DIAGNOSIS; METHODOLOGY; PRIORITY JOURNAL; QUALITY CONTROL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STATISTICAL DISTRIBUTION; STATISTICAL MODEL; UPREGULATION;

EID: 0042093637     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg165     Document Type: Article

References (45)

1. Aharoni,A., Keizer,L.C.P., Bouwneester,H.J., Sun,Z. et al. (1975) Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. The Plant Cell, 12, 647-661.
2. Bischoff,F., Yim,S., Pathak,S., Grant,G., Siciliano,M., Giovanella,B, Strong,L. and Tainsky,M. (1990) Spontateous abnormalities in normal fibroblasts from patient with Li-Fraumeni cancer syndrome: aneuploidy and immortalization. Cancer Res., 24, 7979-7984.
3. Black,M.A. and Doerge,R.W. (2002) Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments. Bioinformatics, 18, 1609-1616.
4. Brazma,A. and Vilo,J. (2000) Gene expression data analysis. FEBS Lett., 480, 17-24.
5. Brody,J.P., Williams,B.A., Wold,B.J. and Quake,S.R. (2002) Significance and statistical errors in the analysis of DNA microarray data. Proc. Natl Acad. Sci. USA, 99, 12975-12978.
6. Chen,Y., Dougherty,E.R. and Bittner,M.L. (1997) Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Optics, 2, 364-374.
7. Claverie,J.-M. (1999) Computational methods for the identification of differential and coordinated gene expression. Hum. Mol. Genet., 8, 1821-1832. Available online at http://biosun01.biostat.jhsph.edu/gparmigi/688/claverie1999.pdf.
8. DeRisi,J.L., Iyer,VR. and Brown,P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
9. DeRisi,J.L., Penland,L., Brown,P.O., Bittner,M.L. et al. (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet., 14, 457-460.
10. Draghici,S. (2002) Statistical intelligence: effective analysis of high-density microarray data. Drug Discovery Today, 7, S55-S63.
11. Dudoit,S., Yang,Y.H., Callow,M. and Speed,T. (2000) Statistical models for identifying differentially expressed genes in replicated cDNA microarray experiments. Technical Report 578, University of California, Berkeley, Available at www.stat.berkeley.edu/tech-reports/index.html.
12. Durbin,B., Hardin,J., Hawkins,D. and Rocke,D. (2002) A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics, 18, S105-S110.
13. Felsenstein,J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
14. Gollahon,L.S., Kraus,E., Wu,T.-A., Yim,S., Strong,L.C., Shay,J.W. and Tainsky,M.A. (1998) Telomerase activity during spontaneous immortalization of Li-Fraumeni syndrome skin fibroblasts. Oncogene, 17, 709-717.
15. Hastie,J., Tibshirani,R., Eisen,M.B., Alizadeh,A., Levy,R., Staudt,L., Chan,W., Botstein,D. and Brown,P. (2000) 'Gene shaving' as a method for indentifying distinct sets of genes with similar expression patterns. Genome Biol., 1, 1-21.
16. Hill,A.A., Hunter,C.P., Tsung,B.T., Tucker-Kellogg,G. and Brown,E.L. (2000) Genomic analysis of gene expression in C.elegans. Science, 290, 809-812.
17. Houts,T.M. (2000) Improved 2-color Exponential normalization for microarray analyses employing cyanine dyes. In Lin,S. (ed.), Procedings of CAMDA 2000, Critical Assesment of Techniques for Microarray Data Mining, December 18-19. Duke University Medical Center, Durham, NC.
18. Hoyle,D.C., Rattray,M., Jupp,R. and Brass,A. (2002) Making sense of microarray data distributions. Bioinformatics, 18, 576-584.
19. Huang,X. and Pan,W. (2002) Comparing three methods for variance estimation with duplicated high-density oligonucleotide arrays. Funct. Integr. Genomics, 2, 126-133.
20. Huber,W., Von Heydebreck,A., Sultmann,H., Poustka,A. and Vingron,M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18, S96-S104.
21. Kerr,M.K. and Churchill,G.A. (2001a) Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc. Natl Acad. Sci. USA, 98, 8961-8965. www.jax.org/research/churchill/pubs/index.html.
22. Kerr,M.K. and Churchill,G.A. (2001b) Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments. Proc. Natl Acad. Sci. USA, 98, 8961-8965. www.jax.org/research/churchill/pubs/index.html.
23. Kerr,M.K. and Churchill,G.A. (2001c) Statistical design and the analysis of gene expression microarray data. Genet. Res., 77, 123-128. www.jax.org/research/churchill/pubs/index.html.
24. Kerr,M.K., Martin,M. and Churchill,G.A. (2000) Analysis of variance for gene expression microarray data. J. Comput. Biol., 7, 819-837.
25. Lee,M.L. and Whitmore,G.A. (2002) Power and sample size for DNA microarray studies. Stat. Med., 21, 3543-3570.
26. Lee,M.-L.T., Kuo,F.C., Whitmore,G.A. and Sklar,J. (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.
27. Love,B., Rank,D.R., Penn,S.G., Jenkins,D.A. and Thomas,R.S. (2002) A conditional density error model for the statistical analysis of microarray data. Bioinformatics, 18, 1064-1072.
28. Mutch,D.M., Berger,A., Mansourian,R., Rytz,A. and Roberts,M.A. (2002) The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data. BMC Bioinformatics, 3, 17- This article is available from: http://www.biomedcentral.com/1471-2105/3/17.
29. Newton,M., Kendziorski,C., Richmond,C., Blattner,F.R. and Tsui,K. (2001) On differential variability of expression ratios: improving statistical inference about gene expresison changes from microarray data. J. Comput. Biol., 8, 37-52.
30. Pan,W. (2002) A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics, 18, 546-554.
31. Richmond,C.S., Glasner,J.D., Mau,R., Jin,H. and Blattner,F.R. (1999) Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res., 27, 3821-3835.
32. Roberts,C.J., Nelson,B., Marton,M.J., Stoughton,R., Meyer,M.R., Bennett,H.A., He,Y.D., Dia,H., Walker,W.L., Hughes,T.R. et al. (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science, 287, 873-880.
33. Sapir,M. and Churchill,G.A. (2000) Estimating the posterior probability of differential gene expression from microarray data. Jackson Labs, Bar Harbor, ME, Technical Report http://www.jax.org/research/churchill/pubs/.
34. Schadt,E.E., Cheng,L., Su,C. and Wong,W.H. (2000) Analyzing high-density oligonucleotide gene expression array data. J. Cell. Biochem., 80, 192-202.
35. Schena,M., Shalon,D., Davis,R. and Brown,P. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
36. Schena,M., Shalon,D., Heller,R., Chai,A., Brown,P. and Davis,R. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl Acad. Sci. USA, 93, 10614-10519.
37. Schuchhardt,J., Beule,D., Wolski,E. and Eickhoff,H. (2000) Normalization strategies for cDNA microarrays. Nucleic Acids Res., 28, e47i-e47v.
38. Sudarsanam,P., Iyer,V.R., Brown,P.O. and Winston,F. (2000) Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 97, 3364-3369.
39. Tao,H., Bausch,C., Richmond,C., Blattner,F.R. and Conway,T. (1999) Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J. Bacteriol., 181, 6425-6440.
40. ter Linde,J.J.M., Liang,H., Davis,R.W., Steensma,H.Y., Dijken,J.P.V. and Pronk,J.T. (1999) Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. J. Bacteriol., 181, 7409-7413.
41. Wellmann,A., Thieblemont,C., Pittaluga,S., Sakai,A. et al. (2000) Detection of differentially expressed genes in lymphomas using cDNA arrays: identification of clusterin as a new diagnostic marker for anaplastic large-cell lymphomas. Blood, 96, 398-404.
42. Wernisch,L., Kendall,S.L., Soneji,S., Wietzorrek,A., Parish,T., Hinds,J., Butcher,P.D. and Stoker,N.G. (2003) Analysis of whole-genome microarray replicates using mixed, models. Bioinformatics, 19, 53-61.
43. White,K.P., Rifkin,S.A., Hurban,P. and Hogness,D.S. (1999) Microarray analysis of Drosophila development during metamorphosis. Science, 286, 2179-2184.
44. Wiens,B.L. (1999) When log-normal and gamma models give different results: a case study. Am. Stat., 53, 89-93.
45. Wildsmith,S.E., Archer,G.E., Winkley,A.J., Lane,P.W. and Bugelski,P.J. (2000) Maximizing of signal derived from cDNA microarrays. Biotechniques, 30, 202-208.