Abstract
Microarray technology allows for the simultaneous profiling of the expression levels of tens of thousands of genes, potentially whole genomes (DeRisi et al. 1997; Lipshutz et al. 1999; Shalon et al. 1996). This unique power has opened the way for new experimental designs that explore the transcriptional profile of cancer and other complex diseases (Alon et al. 1999; Golub et al. 1999; Perou et al. 1999; Schummer et al. 1999; Alizadeh et al. 2000; Bittner et al. 2000; Perou et al. 2000; Ross et al. 2000).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos I S, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403 (6769): 503–511
Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96 (12): 6745–6750
Baldi P, Long A (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509–519
Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Computat Biol 6(30: 281–297
Ben-Dor A, Friedman N, Yakhini Z (2001) Overabundance analysis and class discovery in gene expression data. A preliminary version appeared in Fifth Annual International Conference on Computational Molecular Biology, 2001 with the title “Class Discovery in Gene Expression Data”. J Computat Biol (in press) @references = Ben-Dor A, Bruhn L, Friedman N, Nachman I, Schummer M, Yakhini Z (2000) Tissue classification with gene expression profiles. J Comput Biol 7:559–584
Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate: a practical and powerful approach to multiple testing. J Royal Stat Soc B 57: 289–300
Bishop CM (1995) Neural Networks for Pattern Recognition. Oxford University Press, Oxford, UK
Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M, Radmacher M, Simon R, Yakhini Z, Ben-Dor A, Sampas N, Dougherty E, Wang E, Marin-cola F, Gooden C, Lueders J, Glatfelter A, Pollock P, Carpten J, Gillanders E, Leja D, Dietrich K, Beaudry C, Berens M, Alberts D, Sondak V (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406 (6795): 536–540
Callow M, Dudoit S, Gong E, Speed T, Rubin E (2000) Microarray expression profiling identifies genes with altered expression in hdl-deficient mice. Genome Research 10: 2022–2029
Cortes C, Vapnik V (1995) Support vector machines. Machin Learn 20: 273–297
DeGroot MH (1986) Probability and statistics. Addison Wesley, Reading, MA DeRisi, J, Iyer V, Brown P (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 282: 699–705
Duda RO, Hart PE (1973) Pattern classification and scene analysis. John Wiley and Sons, New York
Dudoit S, Fridlyand J, Speed TP (2000) Comparison of discrimination methods for the classification of tumors using gene expression data. Technical report, UC Berkeley
Durrett R (1991) Probability theory and examples. Wadsworth and Brooks, Cole, California
Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95 (25): 14863–14868
Friedman N, Barash Y, Ben-Dor A, Yakhini Z, Kaminski N (2001) Analysis of non small cell lung cancer transcriptional profiles. In: Chakravarti A, Eisen M, Zhang M (eds) Integrating genome sequence, sequence variation and gene expression. Cold Spring Harbor Laboratories
Furey T, Cristianini N, Duffy N, Bednarski D, Schummer M, Haussier D (2000) Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 16: 906–914
Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek 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 (5439): 531–537
Khan J, Wei J, Ringner M, Saal L, Ladanyi M, Westermann F, Berthold F, Schwab M, Antonescu C, Peterson C, Meltzer P (2001) Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 7: 673–679
Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genet 21(1 Suppl):20–24 Mitchell T ( 1997 ) Machine Learning. McGraw Hill
Perou CM, Jeffrey SS, van de Rijn M, Rees CA, Eisen MB, Ross DT, Pergamenschikov A, Williams CF, Zhu SX, Lee JC, Lashkari D, Shalon D, Brown PO, Botstein D (1999) Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA 96 (16): 9212–9217
Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D (2000) Molecular portraits of human breast tumours. Nature 406 (6797): 747–52
Ripley BD (1996) Pattern recognition and neural networks. Cambridge University Press, Cambridge
Rose K, Gurewitz E, Fox G (1990) Statistical mechanics and phase transitions in clustering. Phys Rev Lett 65: 945–948
Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24 (3): 227–235
Schummer M, Ng WV, Bumgamer RE, Nelson PS, Schummer B, Bednarski DW, Hassell L, Baldwin RL, Karlan BY, Hood L (1999) Comparative hybridization of an array of 21,500 ovarian cDNAs for the discovery of genes overexpressed in ovarian carcinomas. Gene 238 (2): 375–385
Shalon D, Smith SJ, Brown PO (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6 (7): 639–645
Sharan R, Shamir R (2000) CLICK: a clustering algorithm with applications to gene expression analysis. In: Bourne P, Gribskov M (eds) Eight International Conference on Intelligent Systems for Molecular Biology
Slonim DK, Tamayo P, Mesirov JP, Golub TR, Lander ES (2000) Class prediction and discovery using gene expression data In Shamir R, Miyano S, Is-trail S, Pevzner P, Waterman M (eds) Fourth Annual International Conference on Computational Molecular Biology
Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96 (6): 2907–2912
Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999) Systematic determination of genetic network architecture. Nature Genetics 22 (3): 281–285
Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116–5121
Vapnik V (1999) Statistical learning theory. John Wiley and Sons, New York
Wang K, Gan L, Jeffery E, Gayle M, Gown AM, Skelly M, Nelson PS, Ng WV, Schummer M, Hood L, Mulligan J (1999) Monitoring gene expression profile changes in ovarian carcinomas using cDNA microarray. Gene 229 (1–2): 101–108
Xing EP, Jordan MI, Karp RM (2001) Feature selection for high-dimensional genomic microarray data. In: Brodley C, Danyluk A (eds) Machine learning: proceedings of the Eighteenth International Conference
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Friedman, N., Kaminski, N. (2002). Statistical Methods for Analyzing Gene Expression Data for Cancer Research. In: Mewes, HW., Seidel, H., Weiss, B. (eds) Bioinformatics and Genome Analysis. Ernst Schering Research Foundation Workshop, vol 38. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-04747-7_6
Download citation
DOI: https://doi.org/10.1007/978-3-662-04747-7_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-662-04749-1
Online ISBN: 978-3-662-04747-7
eBook Packages: Springer Book Archive