Global gene expression profiling: A complement to conventional histopathologic analysis of neoplasia

Veterinary Pathology

Volumn 42, Issue 6, 2005, Pages 735-752

  Nambiar, P R ^a   Boutin, S R ^a   Raja, R ^b   Rosenberg, D W ^c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b Arcturus Bioscience Inc   (United States)

^c UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

Cancer; Gene expression; Laser capture microdissection; Microarray; Review; Rna linear amplification; Veterinary

Indexed keywords

ANIMAL; ANIMAL DISEASE; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENETICS; IMAGE PROCESSING; LASER; METABOLISM; METHODOLOGY; MICROARRAY ANALYSIS; MICRODISSECTION; NEOPLASM; REVIEW; SPECIES DIFFERENCE; VETERINARY MEDICINE;

ANIMALS; GENE EXPRESSION PROFILING; IMAGE PROCESSING, COMPUTER-ASSISTED; LASERS; MICROARRAY ANALYSIS; MICRODISSECTION; NEOPLASMS; SPECIES SPECIFICITY; VETERINARY MEDICINE;

EID: 28144457268     PISSN: 03009858     EISSN: 03009858     Source Type: Journal    
DOI: 10.1354/vp.42-6-735     Document Type: Review

References (135)

1. Abadie JJ, Amardeilh MA, Delverdier ME: Immunohistochemical detection of proliferating cell nuclear antigen and Ki-67 in mast cell tumors from dogs. J Am Vet Med Assoc 215:1629-1634, 1999
2. Affolter VK, Moore PF: Localized and disseminated histiocytic sarcoma of dendritic cell origin in dogs. Vet Pathol 39:74-83, 2002
3. 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 403:503-511, 2000
4. Alizadeh AA, Staudt LM: Genomic-scale gene expression profiling of normal and malignant immune cells. Curr Opin Immunol 12:219-225, 2000
5. Allred DC, Mohsin SK, Fuqua SA: Histological and biological evolution of human premalignant breast disease. Endocr Relat Cancer 8:47-61, 2001
6. Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96:6745-6750, 1999
7. Anonymous: Microarray standards at last. Nature 419:323, 2002
8. Asakura M, Takashima S, Asano Y, Honma T, Asanuma H, Sanada S, Shintani Y, Liao Y, Kim J, Ogita H, Node K, Minamino T, Yorikane R, Agai A, Kitamura S, Tomoike H, Hori M, Kitakaze M: Canine DNA array as a potential tool for combining physiology and molecular biology. Circ J 67:788-792, 2003
9. Aune TM, Maas K, Moore JH, Olsen NJ: Gene expression profiles in human autoimmune disease. Curr Pharm Des 9:1905-1917, 2003
10. Balkovetz DF, Gerrard ER Jr, Li S, Johnson D, Lee J, Tobias JW, Rogers KK, Snyder RW, Lipschutz JH: Gene expression alterations during HGF-induced dedifferentiation of a renal tubular epithelial cell line (MDCK) using a novel canine DNA microarray. Am J Physiol Renal Physiol 286:F702-F710, 2004
11. Band MR, Olmstead C, Everts RE, Liu ZL, Lewin HA: A 3800 gene microarray for cattle functional genomics: comparison of gene expression in spleen, placenta, and brain. Anim Biotechnol 13:163-172, 2002
12. Barczak A, Rodriguez MW, Hanspers K, Koth LL, Tai YC, Bolstad BM, Speed TP, Erle DJ: Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res 13:1775-1785, 2003
13. Basset DE Jr, Eisen MB, Boguski MS: Gene expression informatics-it's all in your mine. Nat Genet 21(Suppl):51-55, 1999
14. Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185-193, 2003
15. Bonner RF, Emmert-Buck M, Cole K, Pohida T, Chuaqui R, Goldstein S, Liotta LA: Laser capture microdissection: molecular analysis of tissue. Science 278:1481, 1483, 1997
16. 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 29:365-371, 2001
17. Brown PO, Botstein D: Exploring the new world of the genome with DNA microarrays. Nat Genet 21:33-37, 1999
18. Bryant PA, Venter D, Robins-Browne R, Curtis N: Chips with everything: DNA microarrays in infectious diseases. Lancet Infect Dis 4:100-111, 2004
19. Bubendorf L, Kononen J, Koivisto P, Schraml P, Moch H, Gasser TC, Willi N, Mihatsch MJ, Sauter G, Kallioniemi OP: Survey of gene amplifications during prostate cancer progression by high-throughout fluorescence in situ hybridization on tissue microarrays. Cancer Res 59:803-806, 1999
20. Bustin SA: Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25:169-193, 2000
21. Chuaqui RF, Bonner RF, Best CJ, Gillespie JW, Flaig MJ, Hewitt SM, Phillips JL, Krizman DB, Tangrea MA, Ahram M, Linehan WM, Knezevic V, Emmert-Buck MR: Post-analysis follow-up and validation of microarray experiments. Nat Genet 32(Suppl):509-514, 2002
22. Clark EA, Golub TR, Lander ES, Hynes RO: Genomic analysis of metastasis reveals an essential role for RhoC. Nature 406:532-535, 2000
23. Clifford CA, Mackin AJ, Henry CJ: Treatment of canine hemangiosarcoma: 2000 and beyond. J Vet Intern Med 14:479-485, 2000
24. Dank G, Lucroy MD, Griffey SM, Gandour-Edwards R, Madewell BR: bcl-2 and MIB-1 labeling indexes in cats with lymphoma. J Vet Intern Med 16:720-725, 2002
25. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM: Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 14:457-460, 1996
26. Desai KV, Kavanaugh CJ, Calvo A, Green JE: Chipping away at breast cancer: insights from microarray studies of human and mouse mammary cancer. Endocr Relat Cancer 9:207-220, 2002
27. Dobson AT, Raja R, Abeyta MJ, Taylor T, Shen S, Haqq C, Pera RA: The unique transcriptome through day 3 of human preimplantation development. Hum Mol Genet 13:1461-1470, 2004
28. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM: Expression profiling using cDNA microarrays. Nat Genet 21:10-14, 1999
29. Ebert BL, Golub TR: Genomic approaches to hematologic malignancies. Blood 104:923-932, 2004
30. Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA: Laser capture microdissection. Science 274:998-1001, 1996
31. Etienne W, Meyer MH, Peppers J, Meyer RA Jr: Comparison of mRNA gene expression by RT-PCR and DNA microarray. Biotechniques 36:618-626, 2004
32. Falkow S: Molecular Koch's postulates applied to microbial pathogenicity. Rev Infect Dis 10 (Suppl 2):S274-S276, 1988
33. Falkow S: Molecular Koch's postulates applied to bacterial pathogenicity - a personal recollection 15 years later. Nat Rev Microbiol 2:67-72, 2004
34. Fearon ER, Vogelstein B: A genetic model for colorectal tumorigenesis. Cell 61:759-767, 1990
35. Fend F, Kremer M, Quintanilla-Martinez L: Laser capture microdissection: methodical aspects and applications with emphasis on immuno-laser capture microdissection. Pathobiology 68:209-214, 2000
36. Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL: Multiplexed biochemical assays with biological chips. Nature 364:555-556, 1993
37. Fuller AP, Palmer-Toy D, Erlander MG, Sgroi DC: Laser capture microdissection and advanced molecular analysis of human breast cancer. J Mammary Gland Biol Neoplasia 8:335-345, 2003
38. Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I: Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA 98:13784-13789, 2001
39. Going JJ, Lamb RF: Practical histological microdissection for PCR analysis. J Pathol 179:121-124, 1996
40. 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 286:531-537, 1999
41. Guda K, Giardina C, Nambiar P, Cui H, Rosenberg DW: Aberrant transforming growth factor-beta signaling in azoxymethane-induced mouse colon tumors. Mol Carcinog 31:204-213, 2001
42. Hansen K, Khanna C: Spontaneous and genetically engineered animal models; use in preclinical cancer drug development. Eur J Cancer 40:858-880, 2004
43. Hartman JLT, Garvik B, Hartwell L: Principles for the buffering of genetic variation. Science 291:1001-1004, 2001
44. Herath CB, Shiojima S, Ishiwata H, Katsuma S, Kadowaki T, Ushizawa K, Imai K, Takahashi T, Hirasawa A, Tsujimoto G, Hashizume K: Pregnancy-associated changes in genome-wide gene expression profiles in the liver of cow throughout pregnancy. Biochem Biophys Res Commun 313:666-680, 2004
45. Higgins MA, Berridge BR, Mills BJ, Schultze AE, Gao H, Searfoss GH, Baker TK, Ryan TP: Gene expression analysis of the acute phase response using a canine microarray. Toxicol Sci 74:470-484, 2003
46. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS: Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342-347, 2001
47. Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E, Ringner M, Sauter G, Monni O, Elkahloun A, Kallioniemi OP, Kallioniemi A: Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res 62:6240-6245, 2002
48. Irish JM, Hovland R, Krutzik PO, Perez OD, Bruserud O, Gjertsen BT, Nolan GP: Single cell profiling of potentiated phospho-protein networks in cancer cells. Cell 118:217-228, 2004
49. Jass JR, Whitehall VL, Young J, Leggett BA: Emerging concepts in colorectal neoplasia. Gastroenterology 123:862-876, 2002
50. Kabbarah O, Pinto K, Mutch DG, Goodfellow PJ: Expression profiling of mouse endometrial cancers microdissected from ethanol-fixed, paraffin-embedded tissues. Am J Pathol 162:755-762, 2003
51. Kato-Maeda M, Gao Q, Small PM: Microarray analysis of pathogens and their interaction with hosts. Cell Microbiol 3:713-719, 2001
52. Kenzelmann M, Klaren R, Hergenhahn M, Bonrouhi M, Grone HJ, Schmid W, Schutz G: High-accuracy ampli-fication of nanogram total RNA amounts for gene profiling. Genomics 83:550-558, 2004
53. Kobaek-Larsen M, Thorup I, Diederichsen A, Fenger C, Hoitinga MR: Review of colorectal cancer and its metastases in rodent models: comparative aspects with those in humans. Comp Med 50:16-26, 2000
54. Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR: Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci USA 101:811-816, 2004
55. Lau WY, Lai PB, Leung MF, Leung BC, Wong N, Chen G, Leung TW, Liew CT: Differential gene expression of hepatocellular carcinoma using cDNA microarray analysis. Oncol Res 12:59-69, 2000
56. Lechner S, Muller-Ladner U, Renke B, Scholmerich J, Ruschoff J, Kullmann F: Gene expression pattern of laser microdissected colonic crypts of adenomas with low grade dysplasia. Gut 52:1148-1153, 2003
57. Lee PS, Shaw LB, Choe LH, Mehra A, Hatzimanikatis V, Lee KH: Insights into the relation between mRNA and protein expression patterns: II. Experimental observations in Escherichia coli. Biotechnol Bioeng 84:834-841, 2003
58. Leung YF, Cavalieri D: Fundamentals of cDNA microarray data analysis. Trends Genet 19:649-659, 2003
59. Li C, Wong WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98:31-36, 2001
60. Li M, Lin YM, Hasegawa S, Shimokawa T, Murata K, Kameyama M, Ishikawa O, Katagiri T, Tsunoda T, Nakamura Y, Furukawa Y: Genes associated with liver metastasis of colon cancer, identified by genome-wide cDNA microarray. Int J Oncol 24:305-312, 2004
61. Liang AP: Analysing differential expression in cancer. Nat Cancer Rev 3:869-876, 2003
62. Lin YM, Furukawa Y, Tsunoda T, Yue CT, Yang KC, Nakamura Y: Molecular diagnosis of colorectal tumors by expression profiles of 50 genes expressed differentially in adenomas and carcinomas. Oncogene 21:4120-4128, 2002
63. Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D, Botstein D, Brown PO, Gilks CB, van de Rijn M: Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. Am J Pathol 163:2383-2395, 2003
64. Lipschultz R: High density oligonucleotide array. Nat Genet 21:20-24, 1999
65. Ljubimova JY, Lakhter AJ, Loksh A, Yong WH, Riedinger MS, Miner JH, Sorokin LM, Ljubimov AV, Black KL: Overexpression of alpha4 chain-containing laminins in human glial tumors identified by gene microarray analysis. Cancer Res 61:5601-5610, 2001
66. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14:1675-1680, 1996
67. Lu J, Liu Z, Xiong M, Wang Q, Wang X, Yang G, Zhao L, Qiu Z, Zhou C, Wu M: Gene expression profile changes in initiation and progression of squamous cell carcinoma of esophagus. Int J Cancer 91:288-294, 2001
68. Ma XJ, Salunga R, Tuggle JT, Gaudet J, Enright E, McQuary P, Payette T, Pistone M, Stecker K, Zhang BM, Zhou YX, Varnholt H, Smith B, Gadd M, Chatfield E, Kessler J, Baer TM, Erlander MG, Sgroi DC: Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 100:5974-5979, 2003
69. Ma XJ, Wang Z, Ryan PD, Isakoff SJ, Barmettler A, Fuller A, Muir B, Mohapatra G, Salunga R, Tuggle JT, Tran Y, Tran D, Tassin A, Amon P, Wang W, Enright E, Stecker K, Estepa-Sabal E, Smith B, Younger J, Balis U, Michaelson J, Bhan A, Habin K, Baer TM, Brugge J, Haber DA, Erlander MG, Sgroi DC: A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 5:607-616, 2004
70. Macy DW: Hematopoietic tumors. In: Small Animal Clinical Oncology, ed. Withrow SJ, McEwen EG, 3rd ed., pp. 667-672. WB Saunders, Philadelphia, PA, 2001
71. Madsen SA, Chang LC, Hickey MC, Rosa GJ, Coussens PM, Burton JL: Microarray analysis of gene expression in blood neutrophils of parturient cows. Physiol Genomics 16:212-221, 2004
72. Markowitz SD, Dawson DM, Willis J, Willson JK: Focus on colon cancer. Cancer Cell 1:233-236, 2002
73. Meeusen EN, Piedrafita D: Exploiting natural immunity to helminth parasites for the development of veterinary vaccines. Int J Parasitol 33:1285-1290, 2003
74. Mehra A, Lee KH, Hatzimanikatis V: Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations. Biotechnol Bioeng 84:822-833, 2003
75. Mennis-Mikulowski A: High quality RNA from cells isolated by laser-capture microdissection. Biotechniques 33:176-179, 2002
76. Mies C: Molecular biological analysis of paraffin-embedded tissues. Hum Pathol 25:555-560, 1994
77. Nambiar PR, Giardina C, Guda K, Aizu W, Raja R, Rosenberg DW: Role of the alternating reading frame (P19)-p53 pathway in an in vivo murine colon tumor model. Cancer Res 62:3667-3674, 2002
78. Nambiar PR, Haines DM, Ellis JA, Kidney BA, Jackson ML: Mutational analysis of tumor suppressor gene p53 in feline vaccine site-associated sarcomas. Am J Vet Res 61:1277-1281, 2000
79. Nambiar PR, Jackson ML, Ellis JA, Chelack BJ, Kidney BA, Haines DM: Immunohistochemical detection of tumor suppressor gene p53 protein in feline injection site-associated sarcomas. Vet Pathol 38:236-238, 2001
80. Nambiar PR, Nakanishi M, Gupta R, Cheung E, Firouzi A, Ma X-J, Flynn C, Dong M, Guda K, Levine J, Raja R, Achenie L, Rosenberg DW: Genetic signatures of high- and low-risk aberrant crypt foci in a mouse model of sporadic colon cancer. Cancer Res 64:6394-6401, 2004
81. Nobis W, Ren X, Suchyta SP, Suchyta TR, Zanella AJ, Coussens PM: Development of a porcine brain cDNA library, EST database, and microarray resource. Physiol Genomics 16:153-159, 2003
82. Notterman DA, Alon U, Sierk AJ, Levine AJ: Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays. Cancer Res 61:3124-3130, 2001
83. Ohyama H, Zhang X, Kohno Y, Alevizos I, Posner M, Wong DT, Todd R: Laser capture microdissection-generated target sample for high-density oligonucleotide array hybridization. Biotechniques 29:530-536, 2000
84. 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 61:2129-2137, 2001
85. Olert J, Wiedorn KH, Goldmann T, Kuhl H, Mehraein Y, Scherthan H, Niketeghad F, Vollmer E, Muller AM, Muller-Navia J: HOPE fixation: a novel fixing method and paraffin-embedding technique for human soft tissues. Pathol Res Pract 197:823-826, 2001
86. Patnaik AK, Ehler WJ, MacEwen EG: Canine cutaneous mast cell tumor: morphologic grading and survival time in 83 dogs. Vet Pathol 21:469-474, 1984
87. 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: Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc Natl Acad Sci USA 96:9212-9217, 1999
88. 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: Molecular portraits of human breast tumours. Nature 406:747-752, 2000
89. Ponce F, Magnol JP, Ledieu D, Marchal T, Turinelli V, Chalvet-Monfray K, Fournel-Fleury C: Prognostic significance of morphological subtypes in canine malignant lymphomas during chemotherapy. Vet J 167:158-166, 2004
90. Prichard R, Tait A: The role of molecular biology in veterinary parasitology. Vet Parasitol 98:169-194, 2001
91. Quackenbush J: Microarray data normalization and transformation. Nat Genet 32(Suppl):496-501, 2002
92. Renehan AG, O'Dwyer ST, Haboubi NJ, Potten CS: Early cellular events in colorectal carcinogenesis. Colorectal Dis 4:76-89, 2002
93. Rhind SM: Veterinary oncological pathology -current and future perspectives. Vet J 163:7-18, 2002
94. Rickman DS, Bobek MP, Misek DE, Kuick R, Blaivas M, Kurnit DM, Taylor J, Hanash SM: Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis. Cancer Res 61:6885-6891, 2001
95. Russo G, Zegar C, Giordano A: Advantages and limitations of microarray technology in human cancer. Oncogene 22:6497-6507, 2003
96. Sallinen SL, Sallinen PK, Haapasalo HK, Helin HJ, Helen PT, Schraml P, Kallioniemi OP, Kononen J: Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. Cancer Res 60:6617-6622, 2000
97. Sanchez-Carbayo M, Cordon-Cardo C: Applications of array technology: identification of molecular targets in bladder cancer. Br J Cancer 89:2172-2177, 2003
98. Sarli G, Preziosi R, Benazzi C, Castellani G, Marcato PS: Prognostic value of histologic stage and proliferative activity in canine malignant mammary tumors. J Vet Diagn Invest 14:25-34, 2002
99. 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 62:2923-2928, 2002
100. Schena M: Genome analysis with gene expression microarrays. Bioessays 18:427-431, 1996
101. Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470, 1995
102. Schutze K, Posl H, Lahr G: Laser micromanipulation systems as universal tools in cellular and molecular biology and in medicine. Cell Mol Biol (Noisy-le-grand) 44:735-746, 1998
103. Searcy G: The hematopoietic system. In: Thomson's Special Veterinary Pathology, ed. McGavin MD, Carlton WW, Zachary JF, 3rd ed., pp. 370-371. Mosby, St. Louis, MO, 2001
104. Shibata D, Hawes D, Li ZH, Hernandez AM, Spruck CH, Nichols PW: Specific genetic analysis of microscopic tissue after selective ultraviolet radiation fractionation and the polymerase chain reaction. Am J Pathol 141:539-543, 1992
105. Shim C, Zhang W, Rhee CH, Lee JH: Profiling of differentially expressed genes in human primary cervical cancer by complementary DNA expression array. Clin Cancer Res 4:3045-3050, 1998
106. Shirota Y, Kaneko S, Honda M, Kawai HF, Kobayashi K: Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays. Hepatology 33:832-840, 2001
107. Shridhar V, Lee J, Pandita A, Iturria S, Avula R, Staub J, Morrissey M, Calhoun E, Sen A, Kalli K, Keeney G, Roche P, Cliby W, Lu K, Schmandt R, Mills GB, Bast RC Jr, James CD, Couch FJ, Hartmann LC, Lillie J, Smith DI: Genetic analysis of early- versus late-stage ovarian tumors. Cancer Res 61:5895-5904, 2001
108. Simone NL, Bonner RF, Gillespie JW, Emmert-Buck MR, Liotta LA: Laser-capture microdissection: opening the microscopic frontier to molecular analysis. Trends Genet 14:272-276, 1998
109. Slonim DK: From patterns to pathways: gene expression data analysis comes of age. Nat Genet 32(Suppl):502-508, 2002
110. Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P: Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20:399-407, 1997
111. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lonning P, Borresen-Dale AL: Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 98:10869-10874, 2001
112. Strefezzi Rde F, Xavier JG, Catao-Dias JL: Morphometry of canine cutaneous mast cell tumors. Vet Pathol 40:268-275, 2003
113. Su A: Large scale-analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 99:4465-4470, 2002
114. Suchyta SP, Sipkovsky S, Halgren RG, Kruska R, Elftman M, Weber-Nielsen M, Vandehaar MJ, Xiao L, Tempelman RJ, Coussens PM: Bovine mammary gene expression profiling using a cDNA microarray enhanced for mammary-specific transcripts. Physiol Genomics 16:8-18, 2003
115. Suchyta SP, Sipkovsky S, Kruska R, Jeffers A, McNulty A, Coussens MJ, Tempelman RJ, Halgren RG, Saama PM, Bauman DE, Boisclair YR, Burton JL, Collier RJ, DePeters EJ, Ferris TA, Lucy MC, McGuire MA, Medrano JF, Overton TR, Smith TP, Smith GW, Sonstegard TS, Spain JN, Spiers DE, Yao J, Coussens PM: Development and testing of a high-density cDNA microarray resource for cattle. Physiol Genomics 15:158-164, 2003
116. Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC: Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31:5676-5684, 2003
117. Tao W, Mallard B, Karrow N, Bridle B: Construction and application of a bovine immune-endocrine cDNA microarray. Vet Immunol Immunopathol 101:1-17, 2004
118. Taylor TB, Nambiar PR, Raja R, Cheung E, Rosenberg DW, Anderegg B: Microgenomics: identification of new expression profiles via small and single-cell sample analyses. Cytometry 59A:254-261, 2004
119. Thomas R, Fiegler H, Ostrander EA, Galibert F, Carter NP, Breen M: A canine cancer-gene microarray for CGH analysis of tumors. Cytogenet Genome Res 102:254-260, 2003
120. Torhost J: Tissue microarrays for rapid linking of molecular changes to clinical end points. Am J Pathol 159:2249-2256, 2001
121. Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116-5121, 2001
122. van de Rijn M, Gilks CB: Applications of microarrays to histopathology. Histopathology 44:97-108, 2004
123. Van Gelder R: Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 87:1663-1667, 1990
124. Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J, Latreille JP, Wilson RK, Ganem D, DeRisi JL: Viral discovery and sequence recovery using DNA microarrays. PLoS Biol 1:E2, 2003
125. Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM: High-fidelity mRNA amplification for gene profiling. Nat Biotechnol 18:457-459, 2000
126. Wang K, Gan L, Jeffery E, Gayle M, Gown AM, Skelly M, Nelson PS, Ng WV, Schummer M, Hood L, Mulligan J: Monitoring gene expression profile changes in ovarian carcinomas using cDNA microarray. Gene 229:101-108, 1999
127. Watanabe T, Wu TT, Catalano PJ, Ueki T, Satriano R, Haller DG, Benson AB 3rd, Hamilton SR: Molecular predictors of survival after adjuvant chemotherapy for colon cancer. N Engl J Med 344:1196-1206, 2001
128. Weiss DJ, Evanson OA, Deng M, Abrahamsen MS: Gene expression and antimicrobial activity of bovine macrophages in response to Mycobacterium avium subsp. paratuberculosis. Vet Pathol 41:326-337, 2004
129. Wilson DL, Buckley MJ, Helliwell CA, Wilson IW: New normalization methods for cDNA microarray data. Bioinformatics 19:1325-1332, 2003
130. Xu J, Stolk JA, Zhang X, Silva SJ, Houghton RL, Matsumura M, Vedvick TS, Leslie KB, Badaro R, Reed SG: Identification of differentially expressed genes in human prostate cancer using subtraction and microarray. Cancer Res 60:1677-1682, 2000
131. Yao J, Burton JL, Saama P, Sipkovsky S, Coussens PM: Generation of EST and cDNA microarray resources for the study of bovine immunobiology. Acta Vet Scand 42:391-405, 2001
132. Zhang H, Yu CY, Singer B, Xiong M: Recursive partitioning for tumor classification with gene expression microarray data. Proc Natl Acad Sci USA 98:6730-6735, 2001
133. Zhou W, Goodman SN, Galizia G, Lieto E, Ferraraccio F, Pignatelli C, Purdie CA, Piris J, Morris R, Harrison DJ, Paty PB, Culliford A, Romans KE, Montgomery EA, Choti MA, Kinzler KW, Vogelstein B: Counting alleles to predict recurrence of early-stage colorectal cancers. Lancet 359:219-225, 2002
134. Zou TT, Selaru FM, Xu Y, Shustova V, Yin J, Mori Y, Shibata D, Sato F, Wang S, Olaru A, Deacu E, Liu TC, Abraham JM, Meltzer SJ: Application of cDNA microarrays to generate a molecular taxonomy capable of distinguishing between colon cancer and normal colon. Oncogene 21:4855-4862, 2002
135. Zuccari DA, Santana AE, Cury PM, Cordeiro JA: Immunocytochemical study of Ki-67 as a prognostic marker in canine mammary neoplasia. Vet Clin Pathol 33:23-28, 2004