Abstract
The fundamental rationale for the use of microarray-based gene expression profiling to characterize biological samples is based in part on the principle that cells, tissues, and perturbations applied to them can be characterized on the basis of their relative expression of genes and transcripts. Different biological states, cell types, and influences can be distinguished based on transcriptional profiles and the change in the relative levels of different genes and gene groups. This genomic expression profile-based discovery of biological states and effector-actions represents an essential element of a systems-based whole-genome approach to characterizing cells and tissues, and differs from the characterization of individual gene expression changes in isolation from one another, and has the potential to increase knowledge in all fields of biomedicine. The past two decades have seen a paradigm shift in which medical genetics has moved from being a tool of the basic investigator to play a role in the mainstream of medical practice. Identification of genetic causal agents of common endocrine disorders, deciphering underlying molecular pathophysiology of known conditions, development of new predictive tests for genetic abnormalities, and applications in the field of therapeutics are some of the implications of this shift. Endocrine systems, in particular, offer tremendous opportunities for the use of genomic analyses to understand physiological and pathological responses and effectors without being biased to a particular gene or set of genes. Therefore, the responses of diverse and potentially diversely affected systems can be broadly evaluated, constrained only by the limitation that there may be either a primary or secondary impact on transcript abundance. This emerging concept—endocrinomics—thus has the potential to significantly impact the field of endocrine research and clinical practice. However, advancements in the field are also limited by problems in collecting comprehensive datasets, the inherent complexity of multiple interacting systems, genetic variations between individuals, and some cumbersomeness associated with expression profiling technology and data analysis itself. This chapter discusses some of the issues to be considered in the design and analysis of microarray experiments for the characterization of endocrine-regulated systems.
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
Feng, X., Y. Jiang, P. Meltzer, and P.M. Yen, Thyroid hormone regulation of hepatic genes in vivo detected by complementary DNA microarray. Mol Endocrinol, 2000. 14(7): p. 947–55.
Dupont, J., J. Khan, B.H. Qu, P. Metzler, L. Helman, and D. LeRoith, Insulin and IGF-1 induce different patterns of gene expression in mouse fibroblast NIH-3T3 cells: identification by cDNA microarray analysis. Endocrinology, 2001. 142(11): p. 4969–75.
Hoos, A., A. Stojadinovic, B. Singh, M.E. Dudas, D.H. Leung, A.R. Shaha, J.P. Shah, ,M.F. Brennan, C. Cordon-Cardo, and R. Ghossein, Clinical significance of molecular expression profiles of Hurthle cell tumors of the thyroid gland analyzed via tissue microarrays. Am J Pathol, 2002. 160(1): p. 175–83.
Lockhart,D.J. and E.A. Winzeler, Genomics, gene expression and DNA arrays. Nature, 2000. 405(6788): p. 827–36.
van’t Veer, L.J., H. Dai, M.J. van de Vijver, Y.D. He, A.A. Hart, M. Mao, H.L. Peterse, K. van der Kooy, M.J. Marton, A.T. Witteveen, G.J. Schreiber, R.M. Kerkhoven, C. Roberts, P.S. Linsley, R. Bernards, and S.H. Friend, Gene expression profiling predicts clinical outcome of breast cancer. Nature, 2002. 415(6871): p. 530–6.
Page, G.P., J.W. Edwards, G.L. Gadbury, P. Yelisetti, J. Wang, P. Trivedi, and D.B. Allison, The PowerAtlas: a power and sample size atlas for microarray experimental design and research. BMC Bioinformatics, 2006. 7: p. 84.
Shi, H. and R. Bressan, RNA extraction. Methods Mol Biol, 2006. 323: p. 345–8.
Staal, F.J., G. Cario, G. Cazzaniga, T. Haferlach, M. Heuser, W.K. Hofmann, K. Mills, M. Schrappe, M. Stanulla, L.U. Wingen, J.J. van Dongen, and B. Schlegelberger, Consensus guidelines for microarray gene expression analyses in leukemia from three European leukemia networks. Leukemia, 2006. 20(8): p. 1385–92.
Stangegaard, M., I.H. Dufva, and M. Dufva, Reverse transcription using random pentadecamer primers increases yield and quality of resulting cDNA. Biotechniques, 2006. 40(5): p. 649–57.
Verhaak, R.G., F.J. Staal, P.J. Valk, B. Lowenberg, M.J. Reinders, and D. de Ridder, The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies. BMC Bioinformatics, 2006. 7: p. 105.
Walter, M.A., D. Seboek, P. Demougin, L. Bubendorf, M. Oberholzer, J. Muller-Brand, and B. Muller, Extraction of high-integrity RNA suitable for microarray gene expression analysis from long-term stored human thyroid tissues. Pathology, 2006. 38(3): p. 249–53.
Wang, H., J.D. Owens, J.H. Shih, M.C. Li, R.F. Bonner, and J.F. Mushinski, Histological staining methods preparatory to laser capture microdissection significantly affect the integrity of the cellular RNA. BMC Genomics, 2006. 7: p. 97.
Qian, X., B.W. Scheithauer, K. Kovacs, and R.V. Lloyd, DNA microarrays: recent developments and applications to the study of pituitary tissues. Endocrine, 2005. 28(1): p. 49–56.
Churchill, G.A., Fundamentals of experimental design for cDNA microarrays. Nat Genet, 2002. 32 Suppl: p. 490–5.
Quackenbush, J., Microarray data normalization and transformation. Nat Genet, 2002. 32 Suppl: p. 496–501.
Geller, S.C., J.P. Gregg, P. Hagerman, and D.M. Rocke, Transformation and normalization of oligonucleotide microarray data. Bioinformatics, 2003. 19(14): p. 1817–23.
Yuen, T., E. Wurmbach, R.L. Pfeffer, B.J. Ebersole, and S.C. Sealfon, Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res, 2002. 30(10): p. e48.
Kacharmina, J.E., P.B. Crino, and J. Eberwine, Preparation of cDNA from single cells and subcellular regions. Methods Enzymol, 1999. 303: p. 3–18.
Allison, D.B., X. Cui, G.P. Page, and M. Sabripour, Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet, 2006. 7(1): p. 55–65.
Dilley, W.G., S. Kalyanaraman, S. Verma, J.P. Cobb, J.M. Laramie, and T.C. Lairmore, Global gene expression in neuroendocrine tumors from patients with the MEN1 syndrome. Mol Cancer, 2005. 4(1): p. 9.
Zanolin, M.E., F. Tosi, G. Zoppini, R. Castello, G. Spiazzi, R. Dorizzi, M. Muggeo, and P. Moghetti, Clustering of cardiovascular risk factors associated with the insulin resistance syndrome: assessment by principal component analysis in young hyperandrogenic women. Diabetes Care, 2006. 29(2) p. 372–8.
Simon, R., M.D. Radmacher, K. Dobbin, and L.M. McShane, Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst, 2003. 95(1): p. 14–8.
Soinov, L.A., M.A. Krestyaninova, and A. Brazma, Towards reconstruction of gene networks from expression data by supervised learning. Genome Biol, 2003. 4(1): p. R6.
Ambroise, C. and G.J. McLachlan, Selection bias in gene extraction on the basis of microarray gene-expression data. Proc Natl Acad Sci U S A, 2002. 99(10): p. 6562–6.
Gentleman, R.C., V.J. Carey, D.M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A.J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J.Y. Yang, and J. Zhang, Bioconductor: open software development for computational biology and bioinformatics. Genome Biol, 2004. 5(10): p. R80.
Dennis, G., Jr., B.T. Sherman, D.A. Hosack, J. Yang, W. Gao, H.C. Lane, and R.A. Lempicki, DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol, 2003. 4(5): p. P3.
Berezikov, E., V. Guryev, and E. Cuppen, CONREAL web server: identification and visualization of conserved transcription factor binding sites. Nucleic Acids Res, 2005. 33(Web server issue): p. W447–50.
Jegga, A.G., A. Gupta, S. Gowrisankar, M.A. Deshmukh, S. Connolly, K. Finley, and B.J. Aronow, CisMols analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes. Nucleic Acids Res, 2005. 33(Web server issue): p. W408–11.
Sharan, R., I. Ovcharenko, A. Ben-Hur, and R.M. Karp, CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics, 2003. 19 Suppl 1: p. i283–91.
Butte, A.J. and I.S. Kohane, Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput, 2000: p. 418–29.
Segal, E., H. Wang, and D. Koller, Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics, 2003. 19 Suppl 1: p. i264–71.
Hartemink, A.J., D.K. Gifford, T.S. Jaakkola, and R.A. Young, Combining location and expression data for principled discovery of genetic regulatory network models. Pac Symp Biocomput, 2002: p. 437–49.
Brazma, A., P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball, H.C. Causton, T. Gaasterland, P. Glenisson, F.C. Holstege, I.F. Kim, V. Markowitz, J.C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo, and M. Vingron, Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet, 2001. 29(4): p. 365–71.
Barrett, T., T.O. Suzek, D.B. Troup, S.E. Wilhite, W.C. Ngau, P. Ledoux, D. Rudnev, A.E. Lash, W. Fujibuchi, and R. Edgar, NCBI GEO: mining millions of expression profiles – database and tools. Nucleic Acids Res, 2005. 33(Database issue): p. D562–6.
Lee, H.K., A.K. Hsu, J. Sajdak, J. Qin, and P. Pavlidis, Coexpression analysis of human genes across many microarray data sets. Genome Res, 2004. 14(6): p. 1085–94.
Chuaqui, R.F., R.F. Bonner, C.J. Best, J.W. Gillespie, M.J. Flaig, S.M. Hewitt, J.L. Phillips, D.B. Krizman, M.A. Tangrea, M. Ahram, W.M. Linehan, V. Knezevic, and M.R. Emmert-Buck, Post-analysis follow-up and validation of microarray experiments. Nat Genet, 2002. 32 Suppl: p. 509–14.
Barnes, M., J. Freudenberg, S. Thompson, B. Aronow, and P. Pavlidis, Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res, 2005. 33(18): p. 5914–23.
Culhane, A.C., G. Perriere, and D.G. Higgins, Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics, 2003. 4: p. 59.
de Reynies, A., D. Geromin, J.M. Cayuela, F. Petel, P. Dessen, F. Sigaux, and D.S. Rickman, Comparison of the latest commercial short and long oligonucleotide microarray technologies. BMC Genomics, 2006. 7: p. 51.
Irizarry, R.A., D. Warren, F. Spencer, I.F. Kim, S. Biswal, B.C. Frank, E. Gabrielson, J.G. Garcia, J. Geoghegan, G. Germino, C. Griffin, S.C. Hilmer, E. Hoffman, A.E. Jedlicka, E. Kawasaki, F. Martinez-Murillo, L. Morsberger, H. Lee, D. Petersen, J. Quackenbush, A. Scott, M. Wilson, Y. Yang, S.Q. Ye, and W. Yu, Multiple-laboratory comparison of microarray platforms. Nat Methods, 2005. 2(5): p. 345–50.
van Ruissen, F., J.M. Ruijter, G.J. Schaaf, L. Asgharnegad, D.A. Zwijnenburg, M. Kool, and F. Baas, Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips. BMC Genomics, 2005. 6: p. 91.
Woo, Y., J. Affourtit, S. Daigle, A. Viale, K. Johnson, J. Naggert, and G. Churchill, A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech, 2004. 15(4): p. 276–84.
Kothapalli, R., S.J. Yoder, S. Mane, and T.P. Loughran, Jr., Microarray results: how accurate are they? BMC Bioinformatics, 2002. 3: p. 22.
Ntzani, E.E. and J.P. Ioannidis, Predictive ability of DNA microarrays for cancer outcomes and correlates: an empirical assessment. Lancet, 2003. 362(9394): p. 1439–44.
Michiels, S., S. Koscielny, and C. Hill, Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet, 2005. 365(9458): p. 488–92.
Chang, H.Y., D.S. Nuyten, J.B. Sneddon, T. Hastie, R. Tibshirani, T. Sorlie, H. Dai, Y.D. He, L.J. van’t Veer, H. Bartelink, M. van de Rijn, P.O. Brown, and M.J. van de Vijver, Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci U S A, 2005. 102(10): p. 3738–43.
Sorlie, T., R. Tibshirani, J. Parker, T. Hastie, J.S. Marron, A. Nobel, S. Deng, H. Johnsen, R. Pesich, S. Geisler, J. Demeter, C.M. Perou, P.E. Lonning, P.O. Brown, A.L. Borresen-Dale, and D. Botstein, Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A, 2003. 100(14): p. 8418–23.
D’Haeseleer, P., How does gene expression clustering work? Nat Biotechnol, 2005. 23(12): p. 1499–501.
Imbeaud, S. and C. Auffray, ‘The 39 steps’ in gene expression profiling: critical issues and proposed best practices for microarray experiments. Drug Discov Today, 2005. 10(17): p. 1175–82.
Robert-Nicoud, M., M. Flahaut, J.M. Elalouf, M. Nicod, M. Salinas, M. Bens, A. Doucet, P. Wincker, F. Artiguenave, J.D. Horisberger, A. Vandewalle, B.C. Rossier, and D. Firsov, Transcriptome of a mouse kidney cortical collecting duct cell line: effects of aldosterone and vasopressin. Proc Natl Acad Sci U S A, 2001. 98(5): p. 2712–6.
Xu, L.L., Y.P. Su, R. Labiche, T. Segawa, N. Shanmugam, D.G. McLeod, J.W. Moul, and S. Srivastava, Quantitative expression profile of androgen-regulated genes in prostate cancer cells and identification of prostate-specific genes. Int J Cancer, 2001. 92(3): p. 322–8.
de Waard, V., B.M. van den Berg, J. Veken, R. Schultz-Heienbrok, H. Pannekoek, and A.J. van Zonneveld, Serial analysis of gene expression to assess the endothelial cell response to an atherogenic stimulus. Gene, 1999. 226(1): p. 1–8.
Datson, N.A., J. van der Perk, E.R. de Kloet, and E. Vreugdenhil, Identification of corticosteroid-responsive genes in rat hippocampus using serial analysis of gene expression. Eur J Neurosci, 2001. 14(4): p. 675–89.
Gruvberger, S., M. Ringner, Y. Chen, S. Panavally, L.H. Saal, A. Borg, M. Ferno, C. Peterson, and P.S. Meltzer, Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res, 2001. 61(16): p. 5979–84.
Suzuki, T., F. Schirra, S.M. Richards, N.S. Treister, M.J. Lombardi, P. Rowley, R.V. Jensen, and D.A. Sullivan, Estrogen’s and progesterone’s impact on gene expression in the mouse lacrimal gland. Invest Ophthalmol Vis Sci, 2006. 47(1): p. 158–68.
Aronow, B.J., B.D. Richardson, and S. Handwerger, Microarray analysis of trophoblast differentiation: gene expression reprogramming in key gene function categories. Physiol Genomics, 2001. 6(2): p. 105–16.
Davies, S., D. Dai, G. Pickett, and K.K. Leslie, Gene regulation profiles by progesterone and dexamethasone in human endometrial cancer Ishikawa H cells. Gynecol Oncol, 2005. 101(1): 62–70.
Hindmarch, C., S. Yao, G. Beighton, J. Paton, and D. Murphy, A comprehensive description of the transcriptome of the hypothalamoneurohypophyseal system in euhydrated and dehydrated rats. Proc Natl Acad Sci U S A, 2006. 103(5): p. 1609–14.
Elfilali, A., S. Lair, C. Verbeke, P. La Rosa, F. Radvanyi, and E. Barillot, ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. Nucleic Acids Res, 2006. 34(Database issue): p. D613–6.
Newman, J.C. and A.M. Weiner, L2L: a simple tool for discovering the hidden significance in microarray expression data. Genome Biol, 2005. 6(9): p. R81.
Rhodes, D.R., J. Yu, K. Shanker, N. Deshpande, R. Varambally, D. Ghosh, T. Barrette, A. Pandey, and A.M. Chinnaiyan, ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia, 2004. 6(1): p. 1–6.
Ball, C.A., I.A. Awad, J. Demeter, J. Gollub, J.M. Hebert, T. Hernandez-Boussard, H. Jin, J.C. Matese, M. Nitzberg, F. Wymore, Z.K. Zachariah, P.O. Brown, and G. Sherlock, The Stanford microarray database accommodates additional microarray platforms and data formats. Nucleic Acids Res, 2005. 33(Database issue): p. D580–2.
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Humana Press
About this chapter
Cite this chapter
Jegga, A.G., Aronow, B.J., Handwerger, S. (2008). Microarray-based Gene Expression Analysis of Endocrine Systems: Principles of Experimental Design and Interpretation. In: Handwerger, S., Aronow, B. (eds) Genomics in Endocrinology. Contemporary Endocrinology. Humana Press. https://doi.org/10.1007/978-1-59745-309-7_1
Download citation
DOI: https://doi.org/10.1007/978-1-59745-309-7_1
Publisher Name: Humana Press
Print ISBN: 978-1-58829-651-1
Online ISBN: 978-1-59745-309-7
eBook Packages: MedicineMedicine (R0)