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. 2004;24(3):213–224. doi: 10.1023/B:JOCI.0000025443.44833.1d

Gene Expression Profiling: From Microarrays to Medicine

Ashani T Weeraratna 1, James E Nagel 1, Valeria de Mello-Coelho 1, Dennis D Taub 1,✉
PMCID: PMC7086522  PMID: 15114052

Abstract

With the mapping of the human genome comes the ability to identify genes of interest in specific diseases and the pathways involved therein. Laboratory technology has evolved in parallel, providing us with the ability to assay thousands of these genes at once, a technique known as microarray analysis. The main #x003Fion that this type of technology raises is how we can apply this powerful technology to clinical medicine. Recently, advances in data analysis, as well as standardization of the technology, have allowed us to examine this #x003Fion, and indeed a few clinical trials currently being performed include microarrays as part of their protocol. In this review we outline the microarray technique and describe these types of studies in further detail.

Keywords: Microarray, clinic gene expression, review

REFERENCES

  • 1.Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science. 1995;270:484–487. doi: 10.1126/science.270.5235.484. [DOI] [PubMed] [Google Scholar]
  • 2.Augenlicht LH, Wahrman MZ, Halsey H, Anderson L, Taylor J, Lipkin M. Expression of cloned sequences in biopsies of human colonic tissue and in colonic carcinoma cells induced to differentiate in vitro. Cancer Res. 1987;47:6017–6021. [PubMed] [Google Scholar]
  • 3.Nakanishi T, Oka T, Akagi T. Recent advances in DNA microarrays. Acta Med Okayama. 2001;55:319–328. doi: 10.18926/AMO/32002. [DOI] [PubMed] [Google Scholar]
  • 4.Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L. Database resources of the National Center for Biotechnology. Nucleic Acids Res. 2003;31:28–33. doi: 10.1093/nar/gkg033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Schulze A, Downward J. Navigating gene expression using microarrays—A technology review. Nat Cell Biol. 2001;3:E190–E195. doi: 10.1038/35087138. [DOI] [PubMed] [Google Scholar]
  • 6.Manduchi E, Scearce LM, Brestelli JE, Grant GR, Kaestner KH, Stoeckert CJ., Jr Comparison of different labeling methods for two-channel high-density microarray experiments. Physiol Genomics. 2002;10:169–179. doi: 10.1152/physiolgenomics.00120.2001. [DOI] [PubMed] [Google Scholar]
  • 7.Bertucci F, Bernard K, Loriod B, Chang YC, Granjeaud S, Birnbaum D, Nguyen C, Peck K, Jordan BR. Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. Hum Mol Genet. 1999;8:1715–1722. doi: 10.1093/hmg/8.9.1715. [DOI] [PubMed] [Google Scholar]
  • 8.Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467–470. doi: 10.1126/science.270.5235.467. [DOI] [PubMed] [Google Scholar]
  • 9.Lennon GG, Lehrach H. Hybridization analyses of arrayed cDNA libraries. Trends Genet. 1991;7:314–317. doi: 10.1016/0168-9525(91)90420-u. [DOI] [PubMed] [Google Scholar]
  • 10.Carr KM, Bittner M, Trent JM. Gene-expression profiling in human cutaneous melanoma. Oncogene. 2003;22:3076–3080. doi: 10.1038/sj.onc.1206448. [DOI] [PubMed] [Google Scholar]
  • 11.Peterson LE. CLUSFAVOR 5.0: Hierarchical cluster and principal-component analysis of microarray-based transcriptional profiles. Genome Biol. 2002;3:SOFTWARE0002. doi: 10.1186/gb-2002-3-7-software0002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Ringner M, Peterson C. Microarray-based cancer diagnosis with artificial neural networks. Biotechniques. 2003;34(Suppl):30–35. [PubMed] [Google Scholar]
  • 13.Ringner M, Peterson C, Khan J. Analyzing array data using supervised methods. Pharmacogenomics. 2002;3:403–415. doi: 10.1517/14622416.3.3.403. [DOI] [PubMed] [Google Scholar]
  • 14.Pietu G, Alibert O, Guichard V, Lamy B, Bois F, Leroy E, Mariage-Sampson R, Houlgatte R, Soularue P, Auffray C. Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array. Genome Res. 1996;6:492–503. doi: 10.1101/gr.6.6.492. [DOI] [PubMed] [Google Scholar]
  • 15.Schuchhardt J, Beule D, Malik A, Wolski E, Eickhoff H, Lehrach H, Herzel H. Normalization strategies for cDNA microarrays. Nucleic Acids Res. 2000;28:E47. doi: 10.1093/nar/28.10.e47. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Herzel H, Beule D, Kielbasa S, Korbel J, Sers C, Malik A, Eickhoff H, Lehrach H, Schuchhardt J. Extracting information from cDNA arrays. Chaos. 2001;11:98–107. doi: 10.1063/1.1336843. [DOI] [PubMed] [Google Scholar]
  • 17.Quackenbush J. Computational analysis of microarray data. Nat Rev Genet. 2001;2:418–427. doi: 10.1038/35076576. [DOI] [PubMed] [Google Scholar]
  • 18.Beissbarth T, Fellenberg K, Brors B, Arribas-Prat R, Boer J, Hauser NC, Scheideler M, Hoheisel JD, Schutz G, Poustka A, Vingron M. Processing and quality control of DNA array hybridization data. Bioinformatics. 2000;16:1014–1022. doi: 10.1093/bioinformatics/16.11.1014. [DOI] [PubMed] [Google Scholar]
  • 19.Piper MD, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J, Pronk JT. Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem. 2002;277:37001–37008. doi: 10.1074/jbc.M204490200. [DOI] [PubMed] [Google Scholar]
  • 20.Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 1998;95:14863–14868. doi: 10.1073/pnas.95.25.14863. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.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, Marincola 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. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 2000;406:536–540. doi: 10.1038/35020115. [DOI] [PubMed] [Google Scholar]
  • 22.Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA. 1999;96:2907–2912. doi: 10.1073/pnas.96.6.2907. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet. 1999;22:281–285. doi: 10.1038/10343. [DOI] [PubMed] [Google Scholar]
  • 24.Sherlock G. Analysis of large-scale gene expression data. Curr Opin Immunol. 2000;12:201–205. doi: 10.1016/s0952-7915(99)00074-6. [DOI] [PubMed] [Google Scholar]
  • 25.Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science. 1999;286:531–537. doi: 10.1126/science.286.5439.531. [DOI] [PubMed] [Google Scholar]
  • 26.Crescenzi M, Giuliani A. The main biological determinants of tumor line taxonomy elucidated by a principal component analysis of microarray data. FEBS Lett. 2001;507:114–118. doi: 10.1016/s0014-5793(01)02973-8. [DOI] [PubMed] [Google Scholar]
  • 27.Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M, Jr, Haussler D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA. 2000;97:262–267. doi: 10.1073/pnas.97.1.262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics. 2000;16:906–914. doi: 10.1093/bioinformatics/16.10.906. [DOI] [PubMed] [Google Scholar]
  • 29.Shipp MA, Ross KN, Tamayo P, Weng AP, Kutok JL, Aguiar RC, Gaasenbeek M, Angelo M, Reich M, Pinkus GS, Ray TS, Koval MA, Last KW, Norton A, Lister TA, Mesirov J, Neuberg DS, Lander ES, Aster JC, Golub TR. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med. 2002;8:68–74. doi: 10.1038/nm0102-68. [DOI] [PubMed] [Google Scholar]
  • 30.Khan J, Wei JS, Ringner M, Saal LH, Ladanyi M, Westermann F, Berthold F, Schwab M, Antonescu CR, Peterson C, Meltzer PS. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med. 2001;7:673–679. doi: 10.1038/89044. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data. J Comput Biol. 2000;7:601–620. doi: 10.1089/106652700750050961. [DOI] [PubMed] [Google Scholar]
  • 32.Broet P, Richardson S, Radvanyi F. Bayesian hierarchical model for identifying changes in gene expression from microarray experiments. J Comput Biol. 2002;9:671–683. doi: 10.1089/106652702760277381. [DOI] [PubMed] [Google Scholar]
  • 33.Carlisle AJ, Prabhu VV, Elkahloun A, Hudson J, Trent JM, Linehan WM, Williams ED, Emmert-Buck MR, Liotta LA, Munson PJ, Krizman DB. Development of a prostate cDNA microarray and statistical gene expression analysis package. Mol Carcinog. 2000;28:12–22. [PubMed] [Google Scholar]
  • 34.Coombes KR, Highsmith WE, Krogmann TA, Baggerly KA, Stivers DN, Abruzzo LV. Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays. J Comput Biol. 2002;9:655–669. doi: 10.1089/106652702760277372. [DOI] [PubMed] [Google Scholar]
  • 35.Lee ML, Kuo FC, Whitmore GA, Sklar J. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA. 2000;97:9834–9839. doi: 10.1073/pnas.97.18.9834. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J. Standards for microarray data. Science. 2002;298:539. doi: 10.1126/science.298.5593.539b. [DOI] [PubMed] [Google Scholar]
  • 37.Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME) toward standards for microarray data. Nat Genet. 2001;29:365–371. doi: 10.1038/ng1201-365. [DOI] [PubMed] [Google Scholar]
  • 38.Roses AD. Pharmacogenetics and the practice of medicine. Nature. 2000;405:857–865. doi: 10.1038/35015728. [DOI] [PubMed] [Google Scholar]
  • 39.McCarthy JJ, Hilfiker R. The use of single-nucleotide polymorphism maps in pharmacogenomics. Nat Biotechnol. 2000;18:505–508. doi: 10.1038/75360. [DOI] [PubMed] [Google Scholar]
  • 40.Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell WR, Windemuth A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schulz V, Drysdale CM, Nandabalan K, Judson RS, Ruano G, Vovis GF. Haplotype variation and linkage disequilibrium in 313 human genes. Science. 2001;293:489–493. doi: 10.1126/science.1059431. [DOI] [PubMed] [Google Scholar]
  • 41.Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 2001;409:928–933. doi: 10.1038/35057149. [DOI] [PubMed] [Google Scholar]
  • 42.Holden AL. The SNP consortium: Summary of a private consortium effort to develop an applied map of the human genome. Biotechniques. 2002;32(Suppl):22–24. [PubMed] [Google Scholar]
  • 43.Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Shaw N, Lane CR, Lim EP, Kalyanaraman N, Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley GQ, Lander ES. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet. 1999;22:231–238. doi: 10.1038/10290. [DOI] [PubMed] [Google Scholar]
  • 44.Wypgant M. SNP market view: Opportunities, technologies, and products. Biotechniques. 2002;32(Suppl):78–86. [PubMed] [Google Scholar]
  • 45.Hirschhorn JN, Sklar P, Lindblad-Toh K, Lim YM, Ruiz-Gutierrez M, Bolk S, Langhorst B, Schaffner S, Winchester E, Lander ES. SBE-TAGS: An array-based method for efficient single-nucleotide polymorphism genotyping. Proc Natl Acad Sci USA. 2000;97:12164–12169. doi: 10.1073/pnas.210394597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 46.Fan JB, Chen X, Halushka MK, Berno A, Huang X, Ryder T, Lipshutz RJ, Lockhart DJ, Chakravarti A. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. 2000;10:853–860. doi: 10.1101/gr.10.6.853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Buetow KH, Edmonson M, MacDonald R, Clifford R, Yip P, Kelley J, Little DP, Strausberg R, Koester H, Cantor CR, Braun A. High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc Natl Acad Sci USA. 2001;98:581–584. doi: 10.1073/pnas.021506298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 48.Lu M, Shortreed MR, Hall JG, Wang L, Berggren T, Stevens PW, Kelso DM, Lyamichev V, Neri B, Smith LM. A surface invasive cleavage assay for highly parallel SNP analysis. Hum Mutat. 2002;19:416–422. doi: 10.1002/humu.10071. [DOI] [PubMed] [Google Scholar]
  • 49.Kohane IS. Bioinformatics and clinical informatics: The imperative to collaborate. J Am Med Inform Assoc. 2000;7:512–516. doi: 10.1136/jamia.2000.0070512. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 50.Ohmine K, Ota J, Ueda M, Ueno S, Yoshida K, Yamashita Y, Kirito K, Imagawa S, Nakamura Y, Saito K, Akutsu M, Mitani K, Kano Y, Komatsu N, Ozawa K, Mano H. Characterization of stage progression in chronic myeloid leukemia by DNA microarray with purified hematopoietic stem cells. Oncogene. 2001;20:8249–8257. doi: 10.1038/sj.onc.1205029. [DOI] [PubMed] [Google Scholar]
  • 51.Zhan F, Hardin J, Kordsmeier B, Bumm K, Zheng M, Tian E, Sanderson R, Yang Y, Wilson C, Zangari M, Anaissie E, Morris C, Muwalla F, van Rhee F, Fassas A, Crowley J, Tricot G, Barlogie B, Shaughnessy J., Jr Global gene expression profiling of multiple myeloma, monoclonal gammopathy of undetermined significance, and normal bone marrow plasma cells. Blood. 2002;99:1745–1757. doi: 10.1182/blood.v99.5.1745. [DOI] [PubMed] [Google Scholar]
  • 52.Korenberg MJ. Prediction of treatment response using gene expression profiles. J Proteome Res. 2002;1:55–61. doi: 10.1021/pr015510m. [DOI] [PubMed] [Google Scholar]
  • 53.van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Bernards R, Friend SH. Expression profiling predicts outcome in breast cancer. Breast Cancer Res. 2002;5:57–58. doi: 10.1186/bcr562. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 54.Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis DN, Mesirov JP, Lander ES, Golub TR. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature. 2002;415:436–442. doi: 10.1038/415436a. [DOI] [PubMed] [Google Scholar]
  • 55.Cunliffe H, Ringnér M, Bilke S, Walker RL, Cheung JM, Chen Y, Meltzer PS. The gene expression response of breast cancer to growth regulators: Patterns and correlation with tumor expression profiles. Cancer Res. 2003;63:7158–7166. [PubMed] [Google Scholar]
  • 56.Murphy GM, Jr, Pollock BG, Kirshner MA, Pascoe N, Cheuk W, Mulsant BH, Reynolds CF., III CYP2D6 genotyping with oligonucleotide microarrays and nortriptyline concentrations in geriatric depression. Neuropsychopharmacology. 2001;25:737–743. doi: 10.1016/S0893-133X(01)00289-5. [DOI] [PubMed] [Google Scholar]
  • 57.Sreekumar R, Halvatsiotis P, Schimke JC, Nair KS. Gene expression profile in skeletal muscle of type 2 diabetes and the effect of insulin treatment. Diabetes. 2002;51:1913–1920. doi: 10.2337/diabetes.51.6.1913. [DOI] [PubMed] [Google Scholar]
  • 58.Sawiris GP, Sherman-Baust CA, Becker KG, Cheadle C, Teichberg D, Morin PJ. Development of a highly specialized cDNA array for the study and diagnosis of epithelial ovarian cancer. Cancer Res. 2002;62:2923–2928. [PubMed] [Google Scholar]
  • 59.Alizadeh A, Eisen M, Davis RE, Ma C, Sabet H, Tran T, Powell JI, Yang L, Marti GE, Moore DT, Hudson JR, Jr, Chan WC, Greiner T, Weisenburger D, Armitage JO, Lossos I, Levy R, Botstein D, Brown PO, Staudt LM. The lymphochip: A specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harb Symp Quant Biol. 1999;64:71–78. doi: 10.1101/sqb.1999.64.71. [DOI] [PubMed] [Google Scholar]
  • 60.Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Jr, 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 P, Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403:503–511. doi: 10.1038/35000501. [DOI] [PubMed] [Google Scholar]
  • 61.An HJ, Cho NH, Lee SY, Kim IH, Lee C, Kim SJ, Mun MS, Kim SH, Jeong JK. Correlation of cervical carcinoma and precancerous lesions with human papillomavirus (HPV) genotypes detected with the HPV DNA chip microarray method. Cancer. 2003;97:1672–1680. doi: 10.1002/cncr.11235. [DOI] [PubMed] [Google Scholar]
  • 62.Kim CJ, Jeong JK, Park M, Park TS, Park TC, Namkoong SE, Park JS. HPV oligonucleotide microarray-based detection of HPV genotypes in cervical neoplastic lesions. Gynecol Oncol. 2003;89:210–217. doi: 10.1016/s0090-8258(02)00069-0. [DOI] [PubMed] [Google Scholar]
  • 63.Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, Tong S, Urbani C, Comer JA, Lim W, Rollin PE, Dowell SF, Ling AE, Humphrey CD, Shieh WJ, Guarner J, Paddock CD, Rota P, Fields B, DeRisi J, Yang JY, Cox N, Hughes JM, LeDuc JW, Bellini WJ, Anderson LJ. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med. 2003;348:1953–1966. doi: 10.1056/NEJMoa030781. [DOI] [PubMed] [Google Scholar]
  • 64.Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci USA. 2002;99:15687–15692. doi: 10.1073/pnas.242579699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 65.Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Penaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, Gunther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 2003;300:1394–1399. doi: 10.1126/science.1085952. [DOI] [PubMed] [Google Scholar]
  • 66.Lewohl JM, Wang L, Miles MF, Zhang L, Dodd PR, Harris RA. Gene expression in human alcoholism: microarray analysis of frontal cortex. Alcohol Clin Exp Res. 2000;24:1873–1882. [PubMed] [Google Scholar]
  • 67.Mayfield RD, Lewohl JM, Dodd PR, Herlihy A, Liu J, Harris RA. Patterns of gene expression are altered in the frontal and motor cortices of human alcoholics. J Neurochem. 2002;81:802–813. doi: 10.1046/j.1471-4159.2002.00860.x. [DOI] [PubMed] [Google Scholar]
  • 68.Barrans JD, Allen PD, Stamatiou D, Dzau VJ, Liew CC. Global gene expression profiling of end-stage dilated cardiomyopathy using a human cardiovascular-based cDNA microarray. Am J Pathol. 2002;160:2035–2043. doi: 10.1016/S0002-9440(10)61153-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 69.Hwang JJ, Allen PD, Tseng GC, Lam CW, Fananapazir L, Dzau VJ, Liew CC. Microarray gene expression profiles in dilated and hypertrophic cardiomyopathic endstage heart failure. Physiol Genomics. 2002;10:31–44. doi: 10.1152/physiolgenomics.00122.2001. [DOI] [PubMed] [Google Scholar]
  • 70.Shalev A, Pise-Masison CA, Radonovich M, Hoffmann SC, Hirshberg B, Brady JN, Harlan DM. Oligonucleotide microarray analysis of intact human pancreatic islets: identification of glucose-responsive genes and a highly regulated TGFbeta signaling pathway. Endocrinology. 2002;43:3695–3698. doi: 10.1210/en.2002-220564. [DOI] [PubMed] [Google Scholar]
  • 71.Sreekumar R, Halvatsiotis P, Schimke JC, Nair KS. Gene expression profile in skeletal muscle of type 2 diabetes and the effect of insulin treatment. Diabetes. 2002;51:1913–1920. doi: 10.2337/diabetes.51.6.1913. [DOI] [PubMed] [Google Scholar]
  • 72.Clement K, Viguerie N, Diehn M, Alizadeh A, Barbe P, Thalamas C, Storey JD, Brown PO, Barsh GS, Langin D. In vivo regulation of human skeletal muscle gene expression by thyroid hormone. Genome Res. 2002;12:281–291. doi: 10.1101/gr.207702. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 73.Guo X, Liao K. Analysis of gene expression profile during 3T3-L1 preadipocyte differentiation. Gene. 2000;251:45–53. doi: 10.1016/s0378-1119(00)00192-x. [DOI] [PubMed] [Google Scholar]
  • 74.Han E, Hilsenbeck SG. Array-based gene expression profiling to study aging. Mech Ageing Dev. 2001;122:999–1018. doi: 10.1016/s0047-6374(01)00215-9. [DOI] [PubMed] [Google Scholar]
  • 75.Ly DH, Lockhart DJ, Lerner RA, Schultz PG. Mitotic misregulation and human aging. Science. 2000;287:2486–2492. doi: 10.1126/science.287.5462.2486. [DOI] [PubMed] [Google Scholar]
  • 76.Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt LM, Brown PO, Relman DA. Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A. 2002;99:972–977. doi: 10.1073/pnas.231625398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 77.Rus V, Atamas SP, Shustova V, Luzina IG, Selaru F, Magder LS, Via CS. Expression of cytokine-and chemokine-related genes in peripheral blood mononuclear cells from lupus patients by cDNA array. Clin Immunol. 2002;102:283–290. doi: 10.1006/clim.2001.5182. [DOI] [PubMed] [Google Scholar]
  • 78.Beitner-Johnson D, Seta K, Yuan Y, Kim H, Rust RT, Conrad PW, Kobayashi S, Millhorn DE. Identification of hypoxia-responsive genes in a dopaminergic cell line by subtractive cDNA libraries and microarray analysis. Parkinsonism Relat Disord. 2001;7:273–281. doi: 10.1016/s1353-8020(00)00070-5. [DOI] [PubMed] [Google Scholar]
  • 79.Lock C, Hermans G, Pedotti R, Brendolan A, Schadt E, Garren H, Langer-Gould A, Strober S, Cannella B, Allard J, Klonowski P, Austin A, Lad N, Kaminski N, Galli SJ, Oksenberg JR, Raine CS, Heller R, Steinman L. Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis. Nat Med. 2002;8:500–508. doi: 10.1038/nm0502-500. [DOI] [PubMed] [Google Scholar]
  • 80.MacDonald TJ, Brown KM, LaFleur B, Peterson K, Lawlor C, Chen Y, Packer RJ, Cogen P, Stephan DA. Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease. Nat Genet. 2001;29:143–152. doi: 10.1038/ng731. [DOI] [PubMed] [Google Scholar]
  • 81.Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Jr, 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. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403:503–511. doi: 10.1038/35000501. [DOI] [PubMed] [Google Scholar]
  • 82.Ohmine K, Ota J, Ueda M, Ueno S, Yoshida K, Yamashita Y, Kirito K, Imagawa S, Nakamura Y, Saito K, Akutsu M, Mitani K, Kano Y, Komatsu N, Ozawa K, Mano H. Characterization of stage progression in chronic myeloid leukemia by DNA microarray with purified hematopoietic stem cells. Oncogene. 2001;20:8249–8257. doi: 10.1038/sj.onc.1205029. [DOI] [PubMed] [Google Scholar]
  • 83.Loftus SK, Chen Y, Gooden G, Ryan JF, Birznieks G, Hilliard M, Baxevanis AD, Bittner M, Meltzer P, Trent J, Pavan W. Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis. Proc Natl Acad Sci U S A. 1999;96:9277–9280. doi: 10.1073/pnas.96.16.9277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 84.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, Marincola 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. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 2000;406:536–540. doi: 10.1038/35020115. [DOI] [PubMed] [Google Scholar]
  • 85.Clark EA, Golub TR, Lander ES, Hynes RO. Genomic analysis of metastasis reveals an essential role for RhoC. Nature. 2000;406:532–535. doi: 10.1038/35020106. [DOI] [PubMed] [Google Scholar]
  • 86.Gupta RA, Polk DB, Krishna U, Israel DA, Yan F, DuBois RN, Peek RM., Jr Activation of peroxisome proliferator-activated receptor gamma suppresses nuclear factor kappa B-mediated apoptosis induced by Helicobacter pylori in gastric epithelial cells. J. Biol Chem. 2001;276:31059–31066. doi: 10.1074/jbc.M104141200. [DOI] [PubMed] [Google Scholar]
  • 87.Yanagawa R, Furukawa Y, Tsunoda T, Kitahara O, Kameyama M, Murata K, Ishikawa O, Nakamura Y. Genome-wide screening of genes showing altered expression in liver metastases of human colorectal cancers by cDNA microarray. Neoplasia. 2001;3:395–401. doi: 10.1038/sj.neo.7900185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 88.Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Kallioniemi OP, Wilfond B, Borg A, Trent J. Gene-expression profiles in hereditary breast cancer. N Engl J Med. 2001;344:539–548. doi: 10.1056/NEJM200102223440801. [DOI] [PubMed] [Google Scholar]
  • 89.Van T Veer LJ, Dai H, Van De Vijver MJ, He YD, Hart A, Mao M, Peterse HL, Van Der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH. Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002;415:530–535. doi: 10.1038/415530a. [DOI] [PubMed] [Google Scholar]
  • 90.Hippo Y, Taniguchi H, Tsutsumi S, Machida N, Chong JM, Fukayama M, Kodama T, Aburatani H. Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res. 2002;62:233–240. [PubMed] [Google Scholar]
  • 91.Okabe H, Satoh S, Kato T, Kitahara O, Yanagawa R, Yamaoka Y, Tsunoda T, Furukawa Y, Nakamura Y. Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: Identification of genes involved in viral carcinogenesis and tumor progression. Cancer Res. 2001;61:2129–2137. [PubMed] [Google Scholar]
  • 92.Bubendorf L, Kolmer M, Kononen J, Koivisto P, Mousses S, Chen Y, Mahlamaki E, Schraml P, Moch H, Willi N, Elkahloun AG, Pretlow TG, Gasser TC, Mihatsch MJ, Sauter G, Kallioniemi OP. Hormone therapy failure in human prostate cancer: analysis by complementary DNA and tissue microarrays. J Natl Cancer Inst. 1999;91:1758–1764. doi: 10.1093/jnci/91.20.1758. [DOI] [PubMed] [Google Scholar]
  • 93.Mousses S, Wagner U, Chen Y, Kim JW, Bubendorf L, Bittner M, Pretlow T, Elkahloun AG, Trepel JB, Kallioniemi OP. Failure of hormone therapy in prostate cancer involves systematic restoration of androgen responsive genes and activation of rapamycin sensitive signaling. Oncogene. 2001;20:6718–6723. doi: 10.1038/sj.onc.1204889. [DOI] [PubMed] [Google Scholar]
  • 94.Skubitz KM, Skubitz AP. Differential gene expression in renal-cell cancer. J Lab Clin Med. 2002;140:52–64. doi: 10.1067/mlc.2002.125213. [DOI] [PubMed] [Google Scholar]
  • 95.Khan J, Simon R, Bittner M, Chen Y, Leighton SB, Pohida T, Smith PD, Jiang Y, Gooden GC, Trent JM, Meltzer PS. Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res. 1998;58:5009–5013. [PubMed] [Google Scholar]
  • 96.Mok SC, Chao J, Skates S, Wong K, Yiu GK, Muto MG, Berkowitz RS, Cramer DW. Prostasin, a potential serum marker for ovarian cancer: Identification through microarray technology. J Natl Cancer Inst. 2001;93:1458–1464. doi: 10.1093/jnci/93.19.1458. [DOI] [PubMed] [Google Scholar]
  • 97.Nuwaysir EF, Bittner M, Trent J, Barrett JC, Afshari CA. Microarrays and toxicology: The advent of toxicogenomics. Mol Carcinog. 1999;24:153–159. doi: 10.1002/(sici)1098-2744(199903)24:3<153::aid-mc1>3.0.co;2-p. [DOI] [PubMed] [Google Scholar]
  • 98.Waring JF, Halbert DN. The promise of toxicogenomics. Curr Opin Mol Ther. 2002;4:229–235. [PubMed] [Google Scholar]

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