Meta- and reanalysis of gene expression profiles of hot and cold thyroid nodules and papillary thyroid carcinoma for gene groups

Journal of Clinical Endocrinology and Metabolism

Volumn 91, Issue 5, 2006, Pages 1934-1942

  Eszlinger, Markus ^a   Wiench, Małgorzata ^b   Jarza̧b, Barbara ^b   Krohn, Knut ^a,c   Beck, Martin ^d   Läuter, Jürgen ^e   Gubała, Elzbieta ^b   Fujarewicz, Krzysztof ^f   Świerniak, Andrzej ^f   Paschke, Ralf ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b INSTITUTE OF ONCOLOGY   (Poland)

^c UNIVERSITY HOSPITAL LEIPZIG   (Germany)

^d Interdisciplinary Center for Bioinformatics   (Germany)

^e OTTO VON GUERICKE UNIVERSITY   (Germany)

^f SILESIAN UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFICIAL INTELLIGENCE; CANCER CLASSIFICATION; CARCINOGENESIS; CLINICAL TRIAL; CONTROLLED CLINICAL TRIAL; CONTROLLED STUDY; GENE EXPRESSION; HORMONE DETERMINATION; HUMAN; HUMAN TISSUE; MEDICAL INSTRUMENTATION; META ANALYSIS; PRIORITY JOURNAL; SYSTEMATIC REVIEW; THYROID NODULE; THYROID PAPILLARY CARCINOMA;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CARCINOMA, PAPILLARY; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; THYROID NEOPLASMS; THYROID NODULE;

EID: 33646402906     PISSN: 0021972X     EISSN: 0021972X     Source Type: Journal    
DOI: 10.1210/jc.2005-1620     Document Type: Article

References (33)

1. Huang Y, Prasad M, Lemon WJ, Hampel H, Wright FA, Kornacker K, LiVolsi V, Frankel W, Kloos RT, Eng C, Pellegata NS, de la Chapelle A 2001 Gene expression in papillary thyroid carcinoma reveals highly consistent profiles. Proc Natl Acad Sci USA 98:15044-15049
2. Giordano TJ, Kuick R, Thomas DG, Misek DE, Vinco M, Sanders D, Zhu Z, Ciampi R, Roh M, Shedden K, Gauger P, Doherty G, Thompson NW, Hanash S, Koenig RJ, Nikiforov YE 2005 Molecular classification of papillary thyroid carcinoma: distinct BRAF, RAS, and RET/PTC mutation-specific gene expression profiles discovered by DNA microarray analysis. Oncogene 24:6646-6656
3. Aldred MA, Ginn-Pease ME, Morrison CD, Popkie AP, Gimm O, Hoang-Vu C, Krause U, Dralle H, Jhiang SM, Plass C, Eng C 2003 Caveolin-1 and caveolin-2, together with three bone morphogenetic protein-related genes, may encode novel tumor suppressors down-regulated in sporadic follicular thyroid carcinogenesis. Cancer Res 63:2864-2871
4. Barden CB, Shister KW, Zhu B, Guiter G, Greenblatt DY, Zeiger MA, Fahey III TJ 2003 Classification of follicular thyroid tumors by molecular signature: results of gene profiling. Clin Cancer Res 9:1792-1800
5. Eszlinger M, Krohn K, Frenzel R, Kropf S, Tonjes A, Paschke R 2004 Gene expression analysis reveals evidence for inactivation of the TGF-β signaling cascade in autonomously functioning thyroid nodules. Oncogene 23:795-804
6. Finley DJ, Arora N, Zhu B, Gallagher L, Fahey III TJ 2004 Molecular profiling distinguishes papillary carcinoma from benign thyroid nodules. J Clin Endocrinol Metab 89:3214-3223
7. Mazzanti C, Zeiger MA, Costouros NG, Umbricht C, Westra WH, Smith D, Somervell H, Bevilacqua G, Alexander HR, Libutti SK, Costourous N 2004 Using gene expression profiling to differentiate benign versus malignant thyroid tumors. Cancer Res 64:2898-2903
8. Frattini M, Ferrario C, Bressan P, Balestra D, De Cecco L, Mondellini P, Bongarzone I, Collini P, Gariboldi M, Pilotti S, Pierotti MA, Greco A 2004 Alternative mutations of BRAF, RET and NTRK1 are associated with similar but distinct gene expression patterns in papillary thyroid cancer. Oncogene 23:7436-7440
9. Eszlinger M, Krohn K, Berger K, Lauter J, Kropf S, Beck M, Fuhrer D, Paschke R 2005 Gene expression analysis reveals evidence for increased expression of cell cycle-associated genes and gq-protein-protein kinase C signaling in cold thyroid nodules. J Clin Endocrinol Metab 90:1163-1170
10. Jarzab B, Wiench M, Fujarewicz K, Simek K, Jarzab M, Oczko-Wojciechowska M, Wloch J, Czarniecka A, Chmielik E, Lange D, Pawlaczek A, Szpak S, Gubala E, Swierniak A 2005 Gene expression profile of papillary thyroid cancer: sources of variability and diagnostic implications. Cancer Res 65:1587-1597
11. Finley DJ, Zhu B, Barden CB, Fahey III TJ 2004 Discrimination of benign and malignant thyroid nodules by molecular profiling. Ann Surg 240:425-436
12. Aldred MA, Huang Y, Liyanarachchi S, Pellegata NS, Gimm O, Jhiang S, Davuluri RV, de la Chapelle A, Eng C 2004 Papillary and follicular thyroid carcinomas show distinctly different microarray expression profiles and can be distinguished by a minimum of five genes. J Clin Oncol 22:3531-3539
13. Lui WO, Foukakis T, Liden J, Thoppe SR, Dwight T, Hoog A, Zedenius J, Wallin G, Reimers M, Larsson C 2005 Expression profiling reveals a distinct transcription signature in follicular thyroid carcinomas with a PAX8-PPAR(γ) fusion oncogene. Oncogene 24:1467-1476
14. Chevillard S, Ugolin N, Vielh P, Ory K, Levalois C, Elliott D, Clayman GL, El Naggar AK 2004 Gene expression profiling of differentiated thyroid neoplasms: diagnostic and clinical implications. Clin Cancer Res 10:6586-6597
15. Yano Y, Uematsu N, Yashiro T, Hara H, Ueno E, Miwa M, Tsujimoto G, Aiyoshi Y, Uchida K 2004 Gene expression profiling identifies platelet-derived growth factor as a diagnostic molecular marker for papillary thyroid carcinoma. Clin Cancer Res 10:2035-2043
16. Weber F, Shen L, Aldred MA, Morrison CD, Frilling A, Saji M, Schuppert F, Broelsch CE, Ringel MD, Eng C 2005 Genetic classification of benign and malignant thyroid follicular neoplasia based on a 3-gene combination. J Clin Endocrinol Metab 90:2512-2521
17. Westfall PH, Young SS 1993 Resampling-based multiple testing: examples and methods for multiple p-value adjustment. New York: John Wiley, Sons
18. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR 2002 GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 31:19-20
19. Fujarewicz K, Wiench M 2003 Selecting differentially expressed genes for colon tumor classification. Int J Applied Math Comp Sci 13:327-335
20. Fujarewicz K, Kimmel M, Rzeszowska-Wolny J, Swierniak A 2003 A note on classification of gene expression data using Support Vector machines. J Biol Systems 11:43-56
21. Vapnik V 1995 The nature of statistical learning theory. New York: Springer-Verlag
22. Guyon I, Weston J, Barnhill S, Vapnik V 2002 Gene selection for cancer classification using support vector machines. Machine Learning 64:389-422
23. Nimgaonkar A, Sanoudou D, Butte AJ, Haslett JN, Kunkel LM, Beggs AH, Kohane IS 2003 Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics 4:27
24. Hwang KB, Kong SW, Greenberg SA, Park PJ 2004 Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics 5:159
25. Melillo RM, Castellone MD, Guarino V, De Falco V, Cirafici AM, Salvatore G, Caiazzo F, Basolo F, Giannini R, Kruhoffer M, Orntoft T, Fusco A, Santoro M 2005 The RET/PTC-RAS-BRAF linear signaling cascade mediates the motile and mitogenic phenotype of thyroid cancer cells. J Clin Invest 115:1068-1081
26. Ciampi R, Knauf JA, Kerler R, Gandhi M, Zhu Z, Nikiforova MN, Rabes HM, Fagin JA, Nikiforov YE 2005 Oncogenic AKAP9-BRAF fusion is a novel mechanism of MAPK pathway activation in thyroid cancer. J Clin Invest 115:94-101
27. Kimura ET, Nikiforova MN, Zhu Z, Knauf JA, Nikiforov YE, Fagin JA 2003 High prevalence of BRAF mutations in thyroid cancer: genetic evidence for constitutive activation of the RET/PTC-RAS-BRAF signaling pathway in papillary thyroid carcinoma. Cancer Res 63:1454-1457
28. Soares P, Trovisco V, Rocha AS, Lima J, Castro P, Preto A, Maximo V, Botelho T, Seruca R, Sobrinho-Simoes M 2003 BRAF mutations and RET/PTC rearrangements are alternative events in the etiopathogenesis of PTC. Oncogene 22:4578-4580
29. Baris O, Savagner F, Nasser V, Loriod B, Granjeaud S, Guyetant S, Franc B, Rodien P, Rohmer V, Bertucci F, Birnbaum D, Malthiery Y, Reynier P, Houlgatte R 2004 Transcriptional profiling reveals coordinated up-regulation of oxidative metabolism genes in thyroid oncocytic tumors. J Clin Endocrinol Metab 89:994-1005
30. Krohn K, Emmrich P, Ott N, Paschke R 1999 Increased thyroid epithelial cell proliferation in toxic thyroid nodules. Thyroid 9:241-246
31. Krohn K, Stricker I, Emmrich P, Paschke R 2003 Cold thyroid nodules show a marked increase in proliferation markers. Thyroid 13:569-575
32. Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush J 2005 Independence and reproducibility across microarray platforms. Nat Methods 2:337-344
33. Sherlock G 2005 Of fish and chips. Nat Methods 2:329-330