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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
http://www-lbit.iro.umontreal.ca/ISMB98/anglais/ontology.html
Lopez AJ (1998) Alternative splicing of Âpre-mRNA: developmental consequences and mechanisms of regulation. Annu Rev Genet 32:279–305
http://www.affymetrix.com/support/technical/technotes/blood_technote.pdf
Churchill GA (2002) Fundamentals of experimental design for cDNA microarrays. Nat Genet 32:490–495
Kerr MK, Churchill GA (2001) Statistical design and the analysis of gene expression microarray data. Genet Res 77(2):123–128
Smyth GK, Yang YH, Speed T (2003) Statistical issues in cDNA microarray data analysis. Methods Mol Biol 224:111–136
Allison D, Cui X, Page G, Sabripour M (2006) Microarray data analysis: from disarray to Âconsolidation and consensus. Nat Rev Genet 7:55–65
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
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470
Schena M (1996) Genome analysis with gene expression microarrays. BioEssays 18:427–431
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
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
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
Klebanov L, Yakovlev A (2007) Is there an alternative to increasing the sample size in microarray studies? Bioinformation 1(10):429–431
Potter JD (2001) At the interfaces of epidemiology, genetics, and genomics. Nat Rev Genet 2:142–147
Potter JD (2003) Epidemiology, cancer genetics and microarrays: making correct inferences, using appropriate designs. Trends Genet 19(12):690–695
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
Schena M (2003) Microarray analysis. Wiley-Liss, Hoboken, NJ. ISBN 9780471414438
Yang YH, Buckley MJ, Speed TP (2001) Analysis of cDNA microarray images. Bioinformatics 2(4):341–349
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
Angulo J, Serra J (2003) Automatic analysis of DNA microarray images using mathematical morphology. Bioinformatics 19(5):553–562
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
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
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
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
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
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
Durbin BP, Hardin JS, Hawkins DM, Rocke DM (2002) A variance estabilizing transformation for gene expression microarray data. Bioinformatics 18:105–110
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
Munson P (2001) A “consistency” test for determining the significance of gene Âexpression changes on replicate samples and two-convenient variance-stabilizing transÂformations. GeneLogic Workshop on Low Level Analysis of Affymetrix GeneChip Data, Nov. 19, Bethesda, MD
Durbin BP, Hardin JS, Hawkins DM, Rocke DM (2002) A variance estabilizing transformation for gene expression microarray data. Bioinformatics 18:105–110
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
Cui X, Kerr M, Churchill G (2003) Transformations for cDNA microarray data. Stat Appl Genet Mol Biol 2(1) Article 4
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
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
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 Âoxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34:267–273
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
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
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
Xiao Y, Frisina R, Gordon A, Klebanov LB, Yakovlev AY (2004) Multivariate search for differentially expressed gene combinations. BMC Bioinform 5(1):164
Dettling M, Gabrielson E, Parmigiani G (2005) Searching for differentially expressed gene combinations. Genome Biol 6:R88
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
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
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
Efron B, Tibshirani R (2007) On testing the significance of sets of genes. Ann Appl Stat 1(1):107–129
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
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
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
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
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
Lander E (1999) Array of hope. Nat Genet (Supplement 21)
Schena M (2003) Microarray analysis preface page XIV. Wiley-Liss, Hoboken, NJ. ISBN 9780471414438
Frantz S (2005) An array of problems. Nat Rev Drug Discov 4:362–363
Cobb K (2006) Re inventing statistics in microarrays: the search for meaning in a vast sea of data. Biomed Comput Rev 2(4):21
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470
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
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
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
Frantz S (2005) An array of problems. Nat Rev Drug Discov 4:362–363
Ioannidis JPA (2005) Microarrays and molecular research: noise discovery? The Lancet 365(9458):454–455
Marshall E (2004) Getting the noise out of gene arrays. Science 306:630–631
Tan PK et al (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31:5676–5684
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
Miklos GL, Maleszka R (2004) Microarray reality checks in the context of a complex disease. Nat Biotechnol 22:615–621
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
MAQC Consortium (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24(9):1151–1161
Bosotti R et al (2007) Cross platform microÂarray analysis for robust identification of Âdifferentially expressed genes. BMC Bioinform 8(Suppl 1):S5
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
Kuo WP et al (2006) A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 24(7):832
Canales RD et al (2007) Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 24(9): 1115
Klebanov L, Yakovlev A (2007) How high is the level of technical noise in microarray data? Biol Direct 2:9
Robinson MD, Speed TP (2007) A comparison of Affymetrix gene expression arrays. BMC Bioinform 15(8):449
Perkel J (2006) Six things you won’t find in the MAQC. Scientist 20(11):68
Klebanov L, Qiu X, Welle S, Yakovlev A (2007) Statistical methods and microarray data. Nat Biotechnol 25:25–26
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
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
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this protocol
Cite this protocol
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
Download citation
DOI: https://doi.org/10.1007/978-1-60327-337-4_2
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-60327-336-7
Online ISBN: 978-1-60327-337-4
eBook Packages: Springer Protocols