Literature

open in new window Alon, U., et al. 1999 Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A 96(12):6745-50

open in new window Arbeitman, M. N., et al. 2002 Gene expression during the life cycle of Drosophila melanogaster. Science 297(5590):2270-5

open in new window Birnbaum, K., et al. 2003 A gene expression map of the Arabidopsis root. Science 302(5652):1956-60

open in new window Chabas, D., et al. 2001 The influence of the proinflammatory cytokine, osteopontin, on autoimmune demyelinating disease. Science 294(5547):1731-5

open in new window Chung, C. H., P. S. Bernard, and C. M. Perou 2002 Molecular portraits and the family tree of cancer. Nat Genet 32 Suppl:533-40

open in new window Dyrskjot, L., et al. 2003 Identifying distinct classes of bladder carcinoma using microarrays. Nat Genet 33(1):90-6

open in new window Enard, W., et al. 2002 Intra- and interspecific variation in primate gene expression patterns. Science 296(5566):340-3

open in new window Furlong, E. E., et al. 2001 Patterns of gene expression during Drosophila mesoderm development. Science 293(5535):1629-33

open in new window Huang, E., et al. 2003 Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat Genet 34(2):226-30

open in new window Huang, P., et al. 2000 Superoxide dismutase as a target for the selective killing of cancer cells. Nature 407(6802):390-5

open in new window Hughes, T. R., et al. 2000 Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 25(3):333-7

open in new windowIyer, V. R., et al. 1999 The transcriptional program in the response of human fibroblasts to serum. Science 283(5398):83-7

open in new window Jin, W., et al. 2001 The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet 29(4):389-95

open in new window Khaitovich, P., et al. 2004 A neutral model of transcriptome evolution. PLoS Biol 2(5):E132

open in new window Kim, S. K., et al. 2001 A gene expression map for Caenorhabditis elegans. Science 293(5537):2087-92

open in new window Lewohl, J. M., et al. 2001 Application of DNA microarrays to study human alcoholism. J Biomed Sci 8(1):28-36

open in new window Lu, P., A. Nakorchevskiy, and E. M. Marcotte 2003 Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci U S A 100(18):10370-5

open in new window Maleck, K., et al. 2000 The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat Genet 26(4):403-10

open in new window Murphy, C. T., et al. 2003 Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature 424(6946):277-83

open in new window Penn, S. G., et al. 2000 Mining the human genome using microarrays of open reading frames. Nat Genet 26(3):315-8

open in new window Pilpel, Y., P. Sudarsanam, and G. M. Church 2001 Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 29(2):153-9

open in new window Pollack, J. R., et al. 1999 Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23(1):41-6

open in new window Quackenbush, J. 2003 Genomics. Microarrays--guilt by association. Science 302(5643):240-1

open in new window Raghuraman, M. K., et al. 2001 Replication dynamics of the yeast genome. Science 294(5540):115-21

open in new window Ramaswamy, S., et al. 2003 A molecular signature of metastasis in primary solid tumors. Nat Genet 33(1):49-54

open in new window Ren, B., et al. 2000 Genome-wide location and function of DNA binding proteins. Science 290(5500):2306-9

open in new window Rifkin, S. A., J. Kim, and K. P. White 2003 Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet 33(2):138-44

open in new window Schena, M., et al. 1995 Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467-70

open in new window Shoemaker, D. D., et al. 2001 Experimental annotation of the human genome using microarray technology. Nature 409(6822):922-7

open in new window Su, A. I., et al. 2002 Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 99(7):4465-70

open in new window Su, A. I., et al. 2004 A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101(16):6062-7

open in new window van 't Veer, L. J., et al. 2002 Gene expression profiling predicts clinical outcome of breast cancer. Nature 415(6871):530-6

open in new window Walker, J. R., et al. 2004 Applications of a rat multiple tissue gene expression data set. Genome Res 14(4):742-9

open in new window White, K. P., et al. 1999 Microarray analysis of Drosophila development during metamorphosis. Science 286(5447):2179-84

open in new window Whitfield, C. W., A. M. Cziko, and G. E. Robinson 2003 Gene expression profiles in the brain predict behavior in individual honey bees. Science 302(5643):296-9

open in new window Ziauddin, J., and D. M. Sabatini 2001 Microarrays of cells expressing defined cDNAs. Nature 411(6833):107-10

open in new window Auer, H., et al. 2003 Chipping away at the chip bias: RNA degradation in microarray analysis. Nat Genet 35(4):292-3

open in new window Brody, J. P., et al. 2002 Significance and statistical errors in the analysis of DNA microarray data. Proc Natl Acad Sci U S A 99(20):12975-8

open in new window Giles, P. J., and D. Kipling 2003 Normality of oligonucleotide microarray data and implications for parametric statistical analyses. Bioinformatics 19(17):2254-62

open in new window Jenssen, T. K., et al. 2002 Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res 30(14):3235-44

open in new window Konig, R., et al. 2004 Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design. Nucleic Acids Res 32(3):e29

open in new window Rajagopalan, D. 2003 A comparison of statistical methods for analysis of high density oligonucleotide array data. Bioinformatics 19(12):1469-76

open in new window Tran, P. H., et al. 2002 Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Res 30(12):e54

open in new window Xu, R., and X. Li 2003 A comparison of parametric versus permutation methods with applications to general and temporal microarray gene expression data. Bioinformatics 19(10):1284-9

PDF open in new window 2002 Affymetrix, Inc. All Rights Reserved. GeneChip Expression Analysis: Data Analysis Fundamentals

PDF open in new window 2002 Affymetrix, Inc. All Rights Reserved. Statistical Algorithms Description Document

Bolstad, B. M. December 7, 2002 Comparing the effects of background, normalization and summarization on gene expression estimates. Manuscript

open in new window Bolstad, B. M., et al. 2003 A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19(2):185-93

open in new window Cope, L. M., et al. 2004 A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 20(3):323-31

open in new window Geller, S. C., et al. 2003 Transformation and normalization of oligonucleotide microarray data. Bioinformatics 19(14):1817-23

open in new window Hubbell, E., W. M. Liu, and R. Mei 2002 Robust estimators for expression analysis. Bioinformatics 18(12):1585-92

open in new window Irizarry, R. A., et al. 2003 Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31(4):e15

open in new window Irizarry, R. A., et al. 2003 Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4(2):249-64

open in new window Jenssen, T. K., et al. 2002 Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res 30(14):3235-44

open in new window Lemon, W. J., S. Liyanarachchi, and M. You 2003 A high performance test of differential gene expression for oligonucleotide arrays. Genome Biol 4(10):R67

open in new window Li, C., and W. Hung Wong 2001 Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2(8):RESEARCH0032

open in new window Li, C., and W. H. Wong 2001 Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A 98(1):31-6

open in new window Liu, W. M., et al. 2002 Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 18(12):1593-9

open in new window Naef, F., et al. 2002 Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays. Genome Biol 3(4):RESEARCH0018

open in new window Pomeroy, S. L., et al. 2002 Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415(6870):436-42

open in new window Quackenbush, J. 2002 Microarray data normalization and transformation. Nat Genet 32 Suppl:496-501

open in new window Sasik, R., E. Calvo, and J. Corbeil 2002 Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model. Bioinformatics 18(12):1633-40

open in new window Smyth, G. K., and T. Speed 2003 Normalization of cDNA microarray data. Methods 31(4):265-73

open in new window Tseng, G. C., et al. 2001 Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 29(12):2549-57

open in new window Yang, I. V., et al. 2002 Within the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol 3(11):research0062

open in new window Yue, H., et al. 2001 An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res 29(8):E41-1

open in new window Armstrong, S. A., et al. 2002 MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet 30(1):41-7

open in new window Chu, S., et al. 1998 The transcriptional program of sporulation in budding yeast. Science 282(5389):699-705

open in new window Cui, X., and G. A. Churchill 2003 Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 4(4):210

open in new window Dudoit, S., and J. Fridlyand 2002 A prediction-based resampling method for estimating the number of clusters in a dataset. Genome Biol 3(7):RESEARCH0036

open in new window Dudoit, S., and J. Fridlyand 2003 Bagging to improve the accuracy of a clustering procedure. Bioinformatics 19(9):1090-9

open in new window Dyrskjot, L., et al. 2003 Identifying distinct classes of bladder carcinoma using microarrays. Nat Genet 33(1):90-6

open in new window Ein-Dor, L., Kela, I., Getz, G., Givol, D., and Domany, E. 2005 Outcome signature genes in breast cancer: is there a unique set? Bioinformatics. 2005 21(2):171-8

open in new window Eisen , M. B., et al. 1998 Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sc U S A 95(25):14863-8

open in new window Getz, G., E. Levine, and E. Domany 2000 Coupled two-way clustering analysis of gene microarray data. Proc Natl Acad Sci U S A 97(22):12079-84

open in new window Getz, G., et al. 2003 Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data. Bioinformatics 19(9):1079-89

open in new window Golub, T. R., et al. 1999 Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439):531-7

open in new window Huang, E., et al. 2003 Gene expression phenotypic models that predict the activity of pathways. Nat Genet 34(2):226-30.

open in new window Kerr, M. K., and G. A. Churchill 2001 Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc Natl Acad Sci U S A 98(16):8961-5

open in new window Kluger, Y., et al. 2003 Spectral biclustering of microarray data: coclustering genes and conditions. Genome Res 13(4):703-16

open in new window Lord, P. W., et al. 2003 Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 19(10):1275-83

open in new window Mata, J., et al. 2002 The transcriptional program of meiosis and sporulation in fission yeast. Nat Genet 32(1):143-7

open in new window McShane, L. M., et al. 2002 Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data. Bioinformatics 18(11):1462-9

open in new window Pomeroy, S. L., et al. 2002 Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415(6870):436-42

open in new window Ramaswamy, S., et al. 2003 A molecular signature of metastasis in primary solid tumors. Nat Genet 33(1):49-54

open in new window Slonim, D. K. 2002 From patterns to pathways: gene expression data analysis comes of age. Nat Genet 32 Suppl:502-8

open in new window Tamayo, P., et al. 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):2907-12

open in new window Toronen, P., et al. 1999 Analysis of gene expression data using self-organizing maps. FEBS Lett 451(2):142-6

open in new window Tsafrir, D., Tsafrir, I., Ein-Dor, L., Zuk, O., Notterman, D.A. and Domany, E. 2005 Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices. Bioinformatics (10):2301-8

open in new window van 't Veer, L. J., et al. 2002 Gene expression profiling predicts clinical outcome of breast cancer. Nature 415(6871):530-6

open in new window Churchill, G. A. 2002 Fundamentals of experimental design for cDNA microarrays. Nat Genet 32 Suppl:490-5

open in new window Foster, W. R., and R. M. Huber 2002 Current themes in microarray experimental design and analysis. Drug Discov Today 7(5):290-2

open in new window Kane, M. D. 2002 Aligning experimental design with bioinformatics analysis to meet discovery research objectives. Cytometry 47(1):50-1

open in new window Kerr, M. K., and G. A. Churchill 2001 Experimental design for gene expression microarrays. Biostatistics 2(2):183-201

open in new window Kerr, M. K., and G. A. Churchill 2001 Statistical design and the analysis of gene expression microarray data. Genet Res 77(2):123-8

open in new window Morrison, D. A., and J. T. Ellis 2003 The design and analysis of microarray experiments: applications in parasitology. DNA Cell Biol 22(6):357-94

open in new window Oleksiak, M. F., G. A. Churchill, and D. L. Crawford 2002 Variation in gene expression within and among natural populations. Nat Genet 32(2):261-6

open in new window Townsend, J. P. 2003 Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 4(1):41

open in new window Yang, M. C., et al. 2003 Microarray experimental design: power and sample size considerations. Physiol Genomics 16(1):24-8

open in new window Yang, Y. H., and T. Speed 2002 Design issues for cDNA microarray experiments. Nat Rev Genet 3(8):579-88