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Where Statistics and Molecular Microarray Experiments Biology Meet

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Statistical Methods for Microarray Data Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 972))

Abstract

This review chapter presents a statistical point of view to microarray experiments with the purpose of understanding the apparent contradictions that often appear in relation to their results. We give a brief introduction of molecular biology for nonspecialists. We describe microarray experiments from their construction and the biological principles the experiments rely on, to data acquisition and analysis. The role of epidemiological approaches and sample size considerations are also discussed.

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References

  1. http://www-lbit.iro.umontreal.ca/ISMB98/anglais/ontology.html

  2. Lopez AJ (1998) Alternative splicing of ­pre-mRNA: developmental consequences and mechanisms of regulation. Annu Rev Genet 32:279–305

    Article  PubMed  CAS  Google Scholar 

  3. http://www.affymetrix.com/support/technical/technotes/blood_technote.pdf

  4. Churchill GA (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32:490–495

    Article  PubMed  CAS  Google Scholar 

  5. Kerr MK, Churchill GA (2001) Statistical design and the analysis of gene expression microarray data. Genet Res 77(2):123–128

    PubMed  CAS  Google Scholar 

  6. Smyth GK, Yang YH, Speed T (2003) Statistical issues in cDNA microarray data analysis. Methods Mol Biol 224:111–136

    PubMed  CAS  Google Scholar 

  7. Allison D, Cui X, Page G, Sabripour M (2006) Microarray data analysis: from disarray to ­consolidation and consensus. Nat Rev Genet 7:55–65

    Google Scholar 

  8. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Yan AS, Trent JM (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 14:457–460

    Article  PubMed  CAS  Google Scholar 

  9. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    Article  PubMed  CAS  Google Scholar 

  10. Schena M (1996) Genome analysis with gene expression microarrays. BioEssays 18:427–431

    Article  PubMed  CAS  Google Scholar 

  11. Chen Y, Dougherty E, Bittner M (1997) Ratio-based decisions and the quantitative analysis of cDNA microarray images. J Biomed Opt 2(4):364–374

    Article  PubMed  CAS  Google Scholar 

  12. Newton M, Kendziorskim M, Richmond C, Blattner F, Tsui K (2001) On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data. J Comput Biol 8(1):37–52

    Article  PubMed  CAS  Google Scholar 

  13. Sapir M, Churchill GA (2000) Estimating the posterior probability of differential gene,expression from microarray data. Poster, The Jackson Laboratory. http://www.jax.org/research/churchill/pubs/marina.pdf

  14. Klebanov L, Yakovlev A (2007) Is there an alternative to increasing the sample size in microarray studies? Bioinformation 1(10):429–431

    Article  PubMed  Google Scholar 

  15. Potter JD (2001) At the interfaces of epidemiology, genetics, and genomics. Nat Rev Genet 2:142–147

    Article  PubMed  CAS  Google Scholar 

  16. Potter JD (2003) Epidemiology, cancer genetics and microarrays: making correct inferences, using appropriate designs. Trends Genet 19(12):690–695

    Article  PubMed  CAS  Google Scholar 

  17. Webb PM, Melissa A, Merritt MA, Boyle MG, Green AC (2007) Microarrays and epidemiology: not the beginning of the end but the end of the beginning. Cancer Epidemiol Biomarkers Prev 16:637–638

    Article  PubMed  Google Scholar 

  18. Schena M (2003) Microarray analysis. Wiley-Liss, Hoboken, NJ. ISBN 9780471414438

    Google Scholar 

  19. Yang YH, Buckley MJ, Speed TP (2001) Analysis of cDNA microarray images. Bioinformatics 2(4):341–349

    PubMed  CAS  Google Scholar 

  20. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30:e15

    Article  PubMed  Google Scholar 

  21. Angulo J, Serra J (2003) Automatic analysis of DNA microarray images using mathematical morphology. Bioinformatics 19(5):553–562

    Article  PubMed  CAS  Google Scholar 

  22. Li Q, Fraley C, Bumgarner R, Yeung K, Raftery A (2005) Donuts, scratches and blanks: robust model-based segmentation of microarray images. Technical Report no. 473. Department of Statistics, University of Washington

    Google Scholar 

  23. Ahmed A, Vias M, Iyer N, Caldas C, Brenton J (2004) Microarray segmentation methods significantly influence data precision. Nucleic Acids Res 32(5):1–7

    Article  Google Scholar 

  24. Wu Z, Irizarry R, Gentleman R, Murillo F, Spencer F (2003) A model based background adjustment for oligonucleotide expression arrays CGRMA-MLE. Technical Report, John Hopkins University, Department of Biostatistics, Baltimore, MD. Working Papers

    Google Scholar 

  25. Irizarry R, Hobbs F, Beaxer-Barclay Y, Antonellis K, Scherf U, Speed T (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249–264

    Article  PubMed  Google Scholar 

  26. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31(4):e15

    Article  PubMed  Google Scholar 

  27. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30:e15

    Article  PubMed  Google Scholar 

  28. Durbin BP, Hardin JS, Hawkins DM, Rocke DM (2002) A variance estabilizing transformation for gene expression microarray data. Bioinformatics 18:105–110

    Article  Google Scholar 

  29. Huber W, Von Heydebreck A, Sultmann H, Poustka A, Vingron M (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18:96–104

    Article  Google Scholar 

  30. Munson P (2001) A “consistency” test for determining the significance of gene ­expression changes on replicate samples and two-convenient variance-stabilizing trans­formations. GeneLogic Workshop on Low Level Analysis of Affymetrix GeneChip Data, Nov. 19, Bethesda, MD

    Google Scholar 

  31. Durbin BP, Hardin JS, Hawkins DM, Rocke DM (2002) A variance estabilizing transformation for gene expression microarray data. Bioinformatics 18:105–110

    Article  Google Scholar 

  32. Huber W, von Heydebreck A, Sueltmann H, Poustka A, Vingron M (2003) Parameter estimation for the calibration and variance stabilization of microarray data. Stat Appl Genet Mol Biol 2:3.1–3.22

    Google Scholar 

  33. Cui X, Kerr M, Churchill G (2003) Transformations for cDNA microarray data. Stat Appl Genet Mol Biol 2(1) Article 4

    Google Scholar 

  34. Bengtsson H, Hössjer O (2006) Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method. BMC Bioinform 7(100):1–18

    Google Scholar 

  35. Gordon A, Glazko G, Qiu X, Yakovlev A (2007) Control of the mean number of false discoveries, Bonferroni and stability of multiple testing. Ann Appl Stat 1(1):179–190

    Article  Google Scholar 

  36. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman BM, Lander ES, Hirschhorn JN, Altshuler D, Groop LC (2003) PGC-1alpha-responsive genes involved in ­oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34:267–273

    Article  PubMed  CAS  Google Scholar 

  37. Lamb J, Ramaswamy S, Ford HL, Contreras B, Martinez RV, Kittrell FS, Zahnow CA, Patterson N, Golub TR, Ewen ME (2003) A mechanism of cyclin D1 action encoded in the patterns of gene expression in human cancer. Cell 114(3):323–334

    Article  PubMed  CAS  Google Scholar 

  38. Majumder PK, Febbo PG, Bikoff R, Berger R, Xue Q, McMahon LM, Manola J, Brugarolas J, McDonnell TJ, Golub TR, Loda M, Lane HA, Sellers WR (2004) mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways. Nat Med 10(6):594–601

    Article  PubMed  CAS  Google Scholar 

  39. Isakoff MS, Sansam CG, Tamayo P, Subramanian A, Evans JA, Fillmore CM, Wang X, Biegel JA, Pomeroy SL, Mesirov JP, Roberts CW (2005) Inactivation of the Snf5 tumor suppressor stimulates cell cycle progression and cooperates with p53 loss in oncogenic transformation. Proc Nat Acad Sci U S A 102(49):17745–17750

    Article  CAS  Google Scholar 

  40. Xiao Y, Frisina R, Gordon A, Klebanov LB, Yakovlev AY (2004) Multivariate search for differentially expressed gene combinations. BMC Bioinform 5(1):164

    Article  Google Scholar 

  41. Dettling M, Gabrielson E, Parmigiani G (2005) Searching for differentially expressed gene combinations. Genome Biol 6:R88

    Article  PubMed  Google Scholar 

  42. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102(43):15545–15550

    Article  PubMed  CAS  Google Scholar 

  43. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ (2005) Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A 102(38):13544–13549

    Article  PubMed  CAS  Google Scholar 

  44. Barry WT, Nobel AB, Wright FA (2005) Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 1(9):1943–1949

    Article  Google Scholar 

  45. Efron B, Tibshirani R (2007) On testing the significance of sets of genes. Ann Appl Stat 1(1):107–129

    Article  Google Scholar 

  46. Klebanov L, Glazko G, Salzman P, Yakovlev A (2007) A multivariate extension of the gene set enrichment analysis. J Bioinform Comput Biol 5(5):1139–1153

    Article  PubMed  CAS  Google Scholar 

  47. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genomewide expression patterns. Proc Natl Acad Sci U S A 95(25):14863–14868

    Article  PubMed  CAS  Google Scholar 

  48. Golub TR, Slonim DK, Tamayo P, Huard C, Gassenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield DD, Lander ES (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(15):531–537

    Article  PubMed  CAS  Google Scholar 

  49. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 96(6):2907–2912

    Article  PubMed  CAS  Google Scholar 

  50. Wen X, Fuhrman S, Michaelis GS, Carri DB, Smith S, Barker SJ, Somogyi R (1998) Large-scale temporal gene expression mapping of central nervous system development. Proc Natl Acad Sci U S A 95:334–339

    Article  PubMed  CAS  Google Scholar 

  51. Lander E (1999) Array of hope. Nat Genet (Supplement 21)

    Google Scholar 

  52. Schena M (2003) Microarray analysis preface page XIV. Wiley-Liss, Hoboken, NJ. ISBN 9780471414438

    Google Scholar 

  53. Frantz S (2005) An array of problems. Nat Rev Drug Discov 4:362–363

    Google Scholar 

  54. Cobb K (2006) Re inventing statistics in microarrays: the search for meaning in a vast sea of data. Biomed Comput Rev 2(4):21

    Google Scholar 

  55. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    Article  PubMed  CAS  Google Scholar 

  56. Golub TR, Slonim DK, Tamayo P, Huard C, Caasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531–537

    Article  PubMed  CAS  Google Scholar 

  57. Sorlie et al (2001) Gene expression patterns of breast carcinomas distinguish tumor subclass with clinical implications. Proc Natl Acad Sci USA 98(19):10869–10874

    Article  PubMed  CAS  Google Scholar 

  58. Petty RD, Kerr KM, Murray GI, Nicolson MC, Rooney PH, Bissett D, Collie-Duguid ES (2006) Tumour transcriptome reveals the predictive and prognostic impact of lysosomal protease inhibitors in non-small-cell lung cancer. J Clin Oncol 24(11):1729–1744

    Article  PubMed  CAS  Google Scholar 

  59. http://www.medicalnewstoday.com/articles/18822.php

  60. Frantz S (2005) An array of problems. Nat Rev Drug Discov 4:362–363

    Google Scholar 

  61. Ioannidis JPA (2005) Microarrays and molecular research: noise discovery? The Lancet 365(9458):454–455

    Google Scholar 

  62. Marshall E (2004) Getting the noise out of gene arrays. Science 306:630–631

    Article  PubMed  CAS  Google Scholar 

  63. Tan PK et al (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31:5676–5684

    Article  PubMed  CAS  Google Scholar 

  64. Miller RM et al (2004) Dysregulation of gene expression in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-lesioned mouse substantia nigra. J Neurosci 24(34):7445

    Article  PubMed  CAS  Google Scholar 

  65. Miklos GL, Maleszka R (2004) Microarray reality checks in the context of a complex disease. Nat Biotechnol 22:615–621

    Article  PubMed  CAS  Google Scholar 

  66. Suárez-Fariñas M, Noggle S, Heke M, Hemmati-Brivanlou, Magnasco M (2005) Comparing independent microarray studies: the case of human embryonic stem cells. BMC Genomics 6(99):1–11

    Google Scholar 

  67. MAQC Consortium (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24(9):1151–1161

    Article  Google Scholar 

  68. Bosotti R et al (2007) Cross platform micro­array analysis for robust identification of ­differentially expressed genes. BMC Bioinform 8(Suppl 1):S5

    Article  Google Scholar 

  69. Wang Y et al (2006) Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays. BMC Genomics 7:59

    Article  PubMed  Google Scholar 

  70. Kuo WP et al (2006) A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 24(7):832

    Article  PubMed  CAS  Google Scholar 

  71. Canales RD et al (2007) Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 24(9): 1115

    Article  Google Scholar 

  72. Klebanov L, Yakovlev A (2007) How high is the level of technical noise in microarray data? Biol Direct 2:9

    Article  PubMed  Google Scholar 

  73. Robinson MD, Speed TP (2007) A comparison of Affymetrix gene expression arrays. BMC Bioinform 15(8):449

    Article  Google Scholar 

  74. Perkel J (2006) Six things you won’t find in the MAQC. Scientist 20(11):68

    Google Scholar 

  75. Klebanov L, Qiu X, Welle S, Yakovlev A (2007) Statistical methods and microarray data. Nat Biotechnol 25:25–26

    Article  PubMed  CAS  Google Scholar 

  76. http://www.microarrays.ca/MAQC_Review_July2007.pdf

  77. Klebanov L, Jordan C, Yakovlev A (2006) A new type of stochastic dependence revealed in gene expression data. Stat Appl Genet Mol Biol 5:1

    Google Scholar 

  78. Klebanov L, Yakovlev A (2007) Diverse correlation structures in gene expression data and their utility in improving statistical inference. Ann Appl Stat 1(2):538–559

    Article  Google Scholar 

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Correspondence to Diana M. Kelmansky .

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Kelmansky, D.M. (2013). Where Statistics and Molecular Microarray Experiments Biology Meet. In: Yakovlev, A., Klebanov, L., Gaile, D. (eds) Statistical Methods for Microarray Data Analysis. Methods in Molecular Biology, vol 972. Humana Press, New York, NY. https://doi.org/10.1007/978-1-60327-337-4_2

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  • DOI: https://doi.org/10.1007/978-1-60327-337-4_2

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