DNA microarray analyses of melanoma gene expression: A decade in the mines

Pigment Cell Research

Volumn 20, Issue 6, 2007, Pages 466-484

  Hoek, Keith S ^a  

^a UNIVERSITY HOSPITAL ZURICH   (Switzerland)

Author keywords

Data mining; Melanoma; Transcription profiling

Indexed keywords

B RAF KINASE; DNA; MELANOCORTIN 1 RECEPTOR;

CANCER PATIENT; CANCER SURVIVAL; CELL TRANSFORMATION; DNA MICROARRAY; GENE DELETION; GENE EXPRESSION; GENETIC HETEROGENEITY; GENETIC TRANSCRIPTION; MELANOCYTE; MELANOMA; MUTATION; PROTEIN DEPLETION; PROTEIN FUNCTION; REVIEW;

CYCLIN-DEPENDENT KINASE INHIBITOR P16; DATA INTERPRETATION, STATISTICAL; DISEASE PROGRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MELANOCYTES; MELANOMA; MOLECULAR SEQUENCE DATA; NEOPLASM METASTASIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTO-ONCOGENE PROTEINS B-RAF; RECEPTOR, MELANOCORTIN, TYPE 1; SURVIVAL RATE;

EID: 35248899866     PISSN: 08935785     EISSN: 16000749     Source Type: Journal    
DOI: 10.1111/j.1600-0749.2007.00412.x     Document Type: Review

References (110)

1. Allison, D.B., Cui, X., Page, G.P. Sabripour, M. (2006). Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet., 7, 55 65.
2. April, C.S. Barsh, G.S. (2006). Skin layer-specific transcriptional profiles in normal and recessive yellow (Mc1re/Mc1re) mice. Pigment Cell Res., 19, 194 205.
3. April, C.S. Barsh, G.S. (2007). Distinct pigmentary and melanocortin 1 receptor-dependent components of cutaneous defense against ultraviolet radiation. PLoS Genet., 3, e9.
4. Bagheri, S., Nosrati, M., Li, S. et al. (2006). Genes and pathways downstream of telomerase in melanoma metastasis. Proc. Natl Acad. Sci. USA, 103, 11306 11311.
5. Baldi, A., Battista, T., De Luca, A. et al. (2003). Identification of genes down-regulated during melanoma progression: a cDNA array study. Exp. Dermatol., 12, 213 218.
6. Benjamini, Y. Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R Stat. Soc. B, 57, 289 300.
7. Berking, C., Takemoto, R., Schaider, H., Showe, L., Satyamoorthy, K., Robbins, P. Herlyn, M. (2001). Transforming growth factor-beta1 increases survival of human melanoma through stroma remodeling. Cancer Res., 61, 8306 8316.
8. Bittner, M., Meltzer, P., Chen, Y. et al. (2000). Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature, 406, 536 540.
9. Bloethner, S., Chen, B., Hemminki, K., Muller-Berghaus, J., Ugurel, S., Schadendorf, D. Kumar, R. (2005). Effect of common B-RAF and N-RAS mutations on global gene expression in melanoma cell lines. Carcinogenesis, 26, 1224 1232.
10. Bloethner, S., Hemminki, K., Thirumaran, R.K., Chen, B., Mueller-Berghaus, J., Ugurel, S., Schadendorf, D. Kumar, R. (2006). Differences in global gene expression in melanoma cell lines with and without homozygous deletion of the CDKN2A locus genes. Melanoma Res., 16, 297 307.
11. Breslow, A. (1978). Tumor thickness in evaluating prognosis of cutaneous melanoma. Ann. Surg., 187, 440.
12. Carreira, S., Goodall, J., Denat, L., Rodriguez, M., Nuciforo, P., Hoek, K.S., Testori, A., Larue, L. Goding, C.R. (2006). Mitf regulation of Dia1 controls melanoma proliferation and invasiveness. Genes Dev., 20, 3426 3439.
13. Cheng, A.J., Liao, S.K., Chow, S.E., Chen, J.K. Wang, T.C. (1997). Differential inhibition of telomerase activity during induction of differentiation in hematopoietic, melanoma, and glioma cells in culture. Biochem. Biophys. Res. Commun., 237, 438 444.
14. Cheng, S.L., Huang Liu, R., Sheu, J.N., Chen, S.T., Sinchaikul, S. Tsay, G.J. (2006). Toxicogenomics of kojic acid on gene expression profiling of A375 human malignant melanoma cells. Biol. Pharm. Bull., 29, 655 669.
15. Cheng, S.L., Liu, R.H., Sheu, J.N., Chen, S.T., Sinchaikul, S. Tsay, G.J. (2007). Toxicogenomics of A375 human malignant melanoma cells treated with arbutin. J. Biomed. Sci., 14, 87 105.
16. Cozzi, S.J., Parsons, P.G., Ogbourne, S.M., Pedley, J. Boyle, G.M. (2006). Induction of senescence in diterpene ester-treated melanoma cells via protein kinase C-dependent hyperactivation of the mitogen-activated protein kinase pathway. Cancer Res., 66, 10083 10091.
17. Curtin, J.A., Fridlyand, J., Kageshita, T. et al. (2005). Distinct sets of genetic alterations in melanoma. N. Engl. J. Med., 353, 2135 2147.
18. Davies, H., Bignell, G.R., Cox, C. et al. (2002). Mutations of the BRAF gene in human cancer. Nature, 417, 949 954.
19. De Wit, P.E., Moretti, S., Koenders, P.G., Weterman, M.A., Van Muijen, G.N., Gianotti, B. Ruiter, D.J. (1992). Increasing epidermal growth factor receptor expression in human melanocytic tumor progression. J. Invest. Dermatol., 99, 168 173.
20. De Wit, N.J., Rijntjes, J., Diepstra, J.H., Van Kuppevelt, T.H., Weidle, U.H., Ruiter, D.J. Van Muijen, G.N. (2005). Analysis of differential gene expression in human melanocytic tumour lesions by custom made oligonucleotide arrays. Br. J. Cancer, 92, 2249 2261.
21. Derisi, J., Penland, L., Brown, P.O., Bittner, M.L., Meltzer, P.S., Ray, M., Chen, Y., Su, Y.A. Trent, J.M. (1996). Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet., 14, 457 460.
22. Dhomen, N. Marais, R. (2007). New insight into BRAF mutations in cancer. Curr. Opin. Genet. Dev., 17, 31 39.
23. Dome, B., Raso, E., Dobos, J. et al. (2005). Parallel expression of alphaIIbbeta3 and alphavbeta3 integrins in human melanoma cells upregulates bFGF expression and promotes their angiogenic phenotype. Int. J. Cancer, 116, 27 35.
24. Dooley, T.P., Curto, E.V., Davis, R.L., Grammatico, P., Robinson, E.S. Wilborn, T.W. (2003). DNA microarrays and likelihood ratio bioinformatic methods: discovery of human melanocyte biomarkers. Pigment Cell Res., 16, 245 253.
25. Dupuy, A. Simon, R.M. (2007). Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J. Natl Cancer Inst., 99, 147 157.
26. Ehlers, J.P., Worley, L., Onken, M.D. Harbour, J.W. (2005). DDEF1 is located in an amplified region of chromosome 8q and is overexpressed in uveal melanoma. Clin. Cancer Res., 11, 3609 3613.
27. Felicetti, F., Bottero, L., Felli, N., Mattia, G., Labbaye, C., Alvino, E., Peschle, C., Colombo, M.P. Care, A. (2004). Role of PLZF in melanoma progression. Oncogene, 23, 4567 4576.
28. Ferrier, C.M., Van Geloof, W.L., De Witte, H.H., Kramer, M.D., Ruiter, D.J. Van Muijen, G.N. (1998). Epitopes of components of the plasminogen activation system are re-exposed in formalin-fixed paraffin sections by different retrieval techniques. J. Histochem. Cytochem., 46, 469 476.
29. Flanagan, N., Healy, E., Ray, A., Philips, S., Todd, C., Jackson, I.J., Birch-Machin, M.A. Rees, J.L. (2000). Pleiotropic effects of the melanocortin 1 receptor (MC1R) gene on human pigmentation. Hum. Mol. Genet., 9, 2531 2537.
30. Folberg, R., Arbieva, Z., Moses, J. et al. (2006). Tumor cell plasticity in uveal melanoma: microenvironment directed dampening of the invasive and metastatic genotype and phenotype accompanies the generation of vasculogenic mimicry patterns. Am. J. Pathol., 169, 1376 1389.
31. Foser, S., Redwanz, I., Ebeling, M., Heizmann, C.W. Certa, U. (2006). Interferon-alpha and transforming growth factor-beta co-induce growth inhibition of human tumor cells. Cell Mol. Life Sci., 63, 2387 2396.
32. Gallagher, W.M., Bergin, O.E., Rafferty, M. et al. (2005). Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies. Carcinogenesis, 26, 1856 1867.
33. Ghosh, R., Nadiminty, N., Fitzpatrick, J.E., Alworth, W.L., Slaga, T.J. Kumar, A.P. (2005a). Eugenol causes melanoma growth suppression through inhibition of E2F1 transcriptional activity. J. Biol. Chem., 280, 5812 5819.
34. Ghosh, S., Rosenthal, R., Zajac, P., Weber, W.P., Oertli, D., Heberer, M., Martin, I., Spagnoli, G.C. Reschner, A. (2005b). Culture of melanoma cells in 3-dimensional architectures results in impaired immunorecognition by cytotoxic T lymphocytes specific for Melan-A/MART-1 tumor-associated antigen. Ann. Surg., 242, 851 857.
35. Ghosh, S., Spagnoli, G.C., Martin, I., Ploegert, S., Demougin, P., Heberer, M. Reschner, A. (2005c). Three-dimensional culture of melanoma cells profoundly affects gene expression profile: a high density oligonucleotide array study. J. Cell. Physiol., 204, 522 531.
36. Gibbons, F.D. Roth, F.P. (2002). Judging the quality of gene expression-based clustering methods using gene annotation. Genome Res., 12, 1574 1581.
37. Govindarajan, B., Sligh, J.E., Vincent, B.J. et al. (2007). Overexpression of Akt converts radial growth melanoma to vertical growth melanoma. J. Clin. Invest., 117, 719 729.
38. Greider, C.W. Blackburn, E.H. (1987). The telomere terminal transferase of Tetrahymena is a ribonucleoprotein enzyme with two kinds of primer specificity. Cell, 51, 887 898.
39. Hafner, C., Breiteneder, H., Ferrone, S. et al. (2005). Suppression of human melanoma tumor growth in SCID mice by a human high molecular weight-melanoma associated antigen (HMW-MAA) specific monoclonal antibody. Int. J. Cancer, 114, 426 432.
40. Haqq, C., Nosrati, M., Sudilovsky, D. et al. (2005). The gene expression signatures of melanoma progression. Proc. Natl Acad. Sci. USA, 102, 6092 6097.
41. Hendrix, M.J., Seftor, E.A., Meltzer, P.S., Gardner, L.M., Hess, A.R., Kirschmann, D.A., Schatteman, G.C. Seftor, R.E. (2001). Expression and functional significance of VE-cadherin in aggressive human melanoma cells: role in vasculogenic mimicry. Proc. Natl Acad. Sci. USA, 98, 8018 8023.
42. Hoek, K., Rimm, D.L., Williams, K.R. et al. (2004). Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. Cancer Res., 64, 5270 5282.
43. Hoek, K.S., Schlegel, N.C., Brafford, P. et al. (2006). Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature. Pigment Cell Res., 19, 290 302.
44. Ioannidis, J.P. (2005a). Microarrays and molecular research: noise discovery?. Lancet, 365, 454 455.
45. Ioannidis, J.P. (2005b). Why most published research findings are false. PLoS Med., 2, e124.
46. Jaeger, J., Koczan, D., Thiesen, H.J., Ibrahim, S.M., Gross, G., Spang, R. Kunz, M. (2007). Gene expression signatures for tumor progression, tumor subtype, and tumor thickness in laser-microdissected melanoma tissues. Clin. Cancer Res., 13, 806 815.
47. Jamshidi-Parsian, A., Dong, Y., Zheng, X., Zhou, H.S., Zacharias, W. McMasters, K.M. (2005). Gene expression profiling of E2F-1-induced apoptosis. Gene, 344, 67 77.
48. Jean, S., Bideau, C., Bellon, L., Halimi, G., De Meo, M., Orsiere, T., Dumenil, G., Berge-Lefranc, J.L. Botta, A. (2001). The expression of genes induced in melanocytes by exposure to 365-nm UVA: study by cDNA arrays and real-time quantitative RT-PCR. Biochim. Biophys. Acta, 1522, 89 96.
49. Jensen, E.H., Lewis, J.M., Mcloughlin, J.M., Alvarado, M.D., Daud, A., Messina, J., Enkemann, S., Yeatman, T.J., Sondak, V.K. Riker, A.I. (2006). Down-regulation of pro-apoptotic genes is an early event in the progression of malignant melanoma. Ann. Surg. Oncol., 14, 1416 1423.
50. Johansson, P., Pavey, S. Hayward, N. (2007). Confirmation of a BRAF mutation-associated gene expression signature in melanoma. Pigment Cell Res., 20, 216 221.
51. Jorgensen, K., Holm, R., Maelandsmo, G.M. Florenes, V.A. (2003). Expression of activated extracellular signal-regulated kinases 1/2 in malignant melanomas: relationship with clinical outcome. Clin. Cancer Res., 9, 5325 5331.
52. Karpf, A.R., Lasek, A.W., Ririe, T.O., Hanks, A.N., Grossman, D. Jones, D.A. (2004). Limited gene activation in tumor and normal epithelial cells treated with the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine. Mol. Pharmacol., 65, 18 27.
53. Kaufmann, W.K., Nevis, K.R., Qu, P. et al. (2007). Defective cell cycle checkpoint functions in melanoma are associated with altered patterns of gene expression. J. Invest. Dermatol., doi:.
54. Kim, N.W., Piatyszek, M.A., Prowse, K.R., Harley, C.B., West, M.D., Ho, P.L., Coviello, G.M., Wright, W.E., Weinrich, S.L. Shay, J.W. (1994). Specific association of human telomerase activity with immortal cells and cancer. Science, 266, 2011 2015.
55. Kim, C.J., Reintgen, D.S. Yeatman, T.J. (2002). The promise of microarray technology in melanoma care. Cancer Control, 9, 49 53.
56. Kunz, M., Moeller, S., Koczan, D., Lorenz, P., Wenger, R.H., Glocker, M.O., Thiesen, H.J., Gross, G. Ibrahim, S.M. (2003). Mechanisms of hypoxic gene regulation of angiogenesis factor Cyr61 in melanoma cells. J. Biol. Chem., 278, 45651 45660.
57. Lin, S.Y., Yang, J.H., Hsia, T.C., Lee, J.H., Chiu, T.H., Wei, Y.H. Chung, J.G. (2005). Effect of inhibition of aloe-emodin on N-acetyltransferase activity and gene expression in human malignant melanoma cells (A375.S2). Melanoma Res., 15, 489 494.
58. Magnoni, C., Tenedini, E., Ferrari, F. et al. (2007). Transcriptional profiles in melanocytes from clinically unaffected skin distinguish the neoplastic growth pattern in patients with melanoma. Br. J. Dermatol., 156, 62 71.
59. Maniotis, A.J., Folberg, R., Hess, A., Seftor, E.A., Gardner, L.M., Pe'er, J., Trent, J.M., Meltzer, P.S. Hendrix, M.J. (1999). Vascular channel formation by human melanoma cells in vivo and in vitro: vasculogenic mimicry. Am. J. Pathol., 155, 739 752.
60. Manten-Horst, E., Danen, E.H., Smit, L., Snoek, M., Le Poole, I.C., Van Muijen, G.N., Pals, S.T. Ruiter, D.J. (1995). Expression of CD44 splice variants in human cutaneous melanoma and melanoma cell lines is related to tumor progression and metastatic potential. Int. J. Cancer, 64, 182 188.
61. Matichard, E., Verpillat, P., Meziani, R. et al. (2004). Melanocortin 1 receptor (MC1R) gene variants may increase the risk of melanoma in France independently of clinical risk factors and UV exposure. J. Med. Genet., 41, e13.
62. Michiels, S., Koscielny, S. Hill, C. (2007). Interpretation of microarray data in cancer. Br. J. Cancer, 96, 1155 1158.
63. Miller, A.J., Du, J., Rowan, S., Hershey, C.L., Widlund, H.R. Fisher, D.E. (2004). Transcriptional regulation of the melanoma prognostic marker melastatin (TRPM1) by MITF in melanocytes and melanoma. Cancer Res., 64, 509 516.
64. Minami, T., Horiuchi, K., Miura, M. et al. (2004). Vascular endothelial growth factor- and thrombin-induced termination factor, down syndrome critical region-1, attenuates endothelial cell proliferation and angiogenesis. J. Biol. Chem., 279, 50537 50554.
65. Mirmohammadsadegh, A., Baer, A., Nambiar, S., Bardenheuer, W. Hengge, U.R. (2004). Rapid identification of dysregulated genes in cutaneous malignant melanoma metastases using cDNA technology. Cells Tissues Organs, 177, 119 123.
66. Moretti, S., Pinzi, C., Berti, E., Spallanzani, A., Chiarugi, A., Boddi, V., Reali, U.M. Giannotti, B. (1997). In situ expression of transforming growth factor beta is associated with melanoma progression and correlates with Ki67, HLA-DR and beta 3 integrin expression. Melanoma Res., 7, 313 321.
67. Mori, T., Kim, J., Yamano, T., Takeuchi, H., Huang, S., Umetani, N., Koyanagi, K. Hoon, D.S. (2005). Epigenetic up-regulation of C-C chemokine receptor 7 and C-X-C chemokine receptor 4 expression in melanoma cells. Cancer Res., 65, 1800 1807.
68. Muthusamy, V., Duraisamy, S., Bradbury, C.M., Hobbs, C., Curley, D.P., Nelson, B. Bosenberg, M. (2006). Epigenetic silencing of novel tumor suppressors in malignant melanoma. Cancer Res., 66, 11187 11193.
69. Niezabitowski, A., Czajecki, K., Rys, J., Kruczak, A., Gruchala, A., Wasilewska, A., Lackowska, B., Sokolowski, A. Szklarski, W. (1999). Prognostic evaluation of cutaneous malignant melanoma: a clinicopathologic and immunohistochemical study. J. Surg. Oncol., 70, 150 160.
70. Okubo, Y., Hamada, J., Takahashi, Y., Tada, M., Tsutsumida, A., Furuuchi, K., Aoyama, T., Sugihara, T. Moriuchi, T. (2002). Transduction of HOXD3-antisense into human melanoma cells results in decreased invasive and motile activities. Clin. Exp. Metastasis, 19, 503 511.
71. Onken, M.D., Worley, L.A., Ehlers, J.P. Harbour, J.W. (2004). Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Res., 64, 7205 7209.
72. Onken, M.D., Worley, L.A., Davila, R.M., Char, D.H. Harbour, J.W. (2006). Prognostic testing in uveal melanoma by transcriptomic profiling of fine needle biopsy specimens. J. Mol. Diagn., 8, 567 573.
73. Packer, L.M., Pavey, S.J., Boyle, G.M., Stark, M.S., Ayub, A.L., Rizos, H. Hayward, N.K. (2007). Gene expression profiling in melanoma identifies novel downstream effectors of p14ARF. Int. J. Cancer, 121, 784 790.
74. Padovan, E., Terracciano, L., Certa, U., Jacobs, B., Reschner, A., Bolli, M., Spagnoli, G.C., Borden, E.C. Heberer, M. (2002). Interferon stimulated gene 15 constitutively produced by melanoma cells induces e-cadherin expression on human dendritic cells. Cancer Res., 62, 3453 3458.
75. Pavey, S., Johansson, P., Packer, L. et al. (2004). Microarray expression profiling in melanoma reveals a BRAF mutation signature. Oncogene, 23, 4060 4067.
76. Pavlidis, P., Li, Q. Noble, W.S. (2003). The effect of replication on gene expression microarray experiments. Bioinformatics, 19, 1620 1627.
77. Pawitan, Y., Michiels, S., Koscielny, S., Gusnanto, A. Ploner, A. (2005). False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics, 21, 3017 3024.
78. Pollock, P.M., Harper, U.L., Hansen, K.S. et al. (2003). High frequency of BRAF mutations in nevi. Nat. Genet., 33, 19 20.
79. Roberts, D.W., Newton, R.A., Beaumont, K.A., Helen Leonard, J. Sturm, R.A. (2006). Quantitative analysis of MC1R gene expression in human skin cell cultures. Pigment Cell Res., 19, 76 89.
80. Rothhammer, T. Bosserhoff, A.K. (2007). Epigenetic events in malignant melanoma. Pigment Cell Res., 20, 92 111.
81. Ryu, B., Kim, D.S., Deluca, A.M. Alani, R.M. (2007). Comprehensive expression profiling of tumor cell lines identifies molecular signatures of melanoma progression. PLoS ONE, 2, e594.
82. Schena, M., Shalon, D., Davis, R.W. Brown, P.O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467 470.
83. Schick, N., Oakeley, E.J., Hynes, N.E. Badache, A. (2004). TEL/ETV6 is a signal transducer and activator of transcription 3 (Stat3)-induced repressor of Stat3 activity. J. Biol. Chem., 279, 38787 38796.
84. Seftor, R.E., Seftor, E.A., Koshikawa, N., Meltzer, P.S., Gardner, L.M., Bilban, M., Stetler-Stevenson, W.G., Quaranta, V. Hendrix, M.J. (2001). Cooperative interactions of laminin 5 gamma2 chain, matrix metalloproteinase-2, and membrane type-1-matrix/metalloproteinase are required for mimicry of embryonic vasculogenesis by aggressive melanoma. Cancer Res., 61, 6322 6327.
85. Seftor, E.A., Meltzer, P.S., Kirschmann, D.A., Pe'er, J., Maniotis, A.J., Trent, J.M., Folberg, R. Hendrix, M.J. (2002). Molecular determinants of human uveal melanoma invasion and metastasis. Clin. Exp. Metastasis, 19, 233 246.
86. Seykora, J.T., Jih, D., Elenitsas, R., Horng, W.H. Elder, D.E. (2003). Gene expression profiling of melanocytic lesions. Am. J. Dermatopathol., 25, 6 11.
87. Shiraishi, K., Yamasaki, K., Nanba, D., Inoue, H., Hanakawa, Y., Shirakata, Y., Hashimoto, K. Higashiyama, S. (2007). Pre-B-cell leukemia transcription factor 1 is a major target of promyelocytic leukemia zinc-finger-mediated melanoma cell growth suppression. Oncogene, 26, 339 348.
88. Silye, R., Karayiannakis, A.J., Syrigos, K.N. et al. (1998). E-cadherin/catenin complex in benign and malignant melanocytic lesions. J. Pathol., 186, 350 355.
89. Smith, A.P., Hoek, K. Becker, D. (2005). Whole-genome expression profiling of the melanoma progression pathway reveals marked molecular differences between nevi/melanoma in situ and advanced-stage melanomas. Cancer Biol. Ther., 4, 1018 1029.
90. Suyama, E., Minoshima, H., Kawasaki, H. Taira, K. (2002). Identification of AP-2-regulated genes by macroarray profiling of gene expression in human A375P melanoma. Nucleic Acids Res. Suppl., 2, 247 248.
91. Talantov, D., Mazumder, A., Yu, J.X., Briggs, T., Jiang, Y., Backus, J., Atkins, D. Wang, Y. (2005). Novel genes associated with malignant melanoma but not benign melanocytic lesions. Clin. Cancer Res., 11, 7234 7242.
92. Tsai, C.A., Hsueh, H.M. Chen, J.J. (2003). Estimation of false discovery rates in multiple testing: application to gene microarray data. Biometrics, 59, 1071 1081.
93. Tsavachidou, D., Coleman, M.L., Athanasiadis, G., Li, S., Licht, J.D., Olson, M.F. Weber, B.L. (2004). SPRY2 is an inhibitor of the ras/extracellular signal-regulated kinase pathway in melanocytes and melanoma cells with wild-type BRAF but not with the V599E mutant. Cancer Res., 64, 5556 5559.
94. Tschentscher, F., Husing, J., Holter, T. et al. (2003). Tumor classification based on gene expression profiling shows that uveal melanomas with and without monosomy 3 represent two distinct entities. Cancer Res., 63, 2578 2584.
95. Vaisanen, A., Kallioinen, M., Taskinen, P.J. Turpeenniemi-Hujanen, T. (1998). Prognostic value of MMP-2 immunoreactive protein (72 kD type IV collagenase) in primary skin melanoma. J. Pathol., 186, 51 58.
96. Valery, C., Grob, J.J. Verrando, P. (2001). Identification by cDNA microarray technology of genes modulated by artificial ultraviolet radiation in normal human melanocytes: relation to melanocarcinogenesis. J. Invest. Dermatol., 117, 1471 1482.
97. Van Belle, P.A., Elenitsas, R., Satyamoorthy, K. et al. (1999). Progression-related expression of beta3 integrin in melanomas and nevi. Hum. Pathol., 30, 562 567.
98. Van Der Velden, P.A., Zuidervaart, W., Hurks, M.H. et al. (2003). Expression profiling reveals that methylation of TIMP3 is involved in uveal melanoma development. Int. J. Cancer, 106, 472 479.
99. Van Kempen, L.C., Van Den Oord, J.J., Van Muijen, G.N., Weidle, U.H., Bloemers, H.P. Swart, G.W. (2000). Activated leukocyte cell adhesion molecule/CD166, a marker of tumor progression in primary malignant melanoma of the skin. Am. J. Pathol., 156, 769 774.
100. Vignjevic, D., Kojima, S., Aratyn, Y., Danciu, O., Svitkina, T. Borisy, G.G. (2006). Role of fascin in filopodial protrusion. J. Cell Biol., 174, 863 875.
101. Vogl, A., Sartorius, U., Vogt, T., Roesch, A., Landthaler, M., Stolz, W. Becker, B. (2005). Gene expression profile changes between melanoma metastases and their daughter cell lines: implication for vaccination protocols. J. Invest. Dermatol., 124, 401 404.
102. Voisey, J., Kelly, G. Van Daal, A. (2003). Agouti signal protein regulation in human melanoma cells. Pigment Cell Res., 16, 65 71.
103. Wang, E., Miller, L.D., Ohnmacht, G.A. et al. (2002). Prospective molecular profiling of melanoma metastases suggests classifiers of immune responsiveness. Cancer Res., 62, 3581 3586.
104. Wang, X., Wang, M., Amarzguioui, M., Liu, F., Fodstad, O. Prydz, H. (2004). Downregulation of tissue factor by RNA interference in human melanoma LOX-L cells reduces pulmonary metastasis in nude mice. Int. J. Cancer, 112, 994 1002.
105. Winnepenninckx, V., Lazar, V., Michiels, S. et al. (2006). Gene expression profiling of primary cutaneous melanoma and clinical outcome. J. Natl Cancer Inst., 98, 472 482.
106. Worley, L.A., Onken, M.D., Person, E., Robirds, D., Branson, J., Char, D.H., Perry, A. Harbour, J.W. (2007). Transcriptomic versus chromosomal prognostic markers and clinical outcome in uveal melanoma. Clin. Cancer Res., 13, 1466 1471.
107. Xi, Y., Nakajima, G., Hamil, T., Fodstad, O., Riker, A. Ju, J. (2006). Association of insulin-like growth factor binding protein-3 expression with melanoma progression. Mol. Cancer Ther., 5, 3078 3084.
108. Yang, G., Zhang, G., Pittelkow, M.R., Ramoni, M. Tsao, H. (2006). Expression profiling of UVB response in melanocytes identifies a set of p53-target genes. J. Invest. Dermatol., 126, 2490 2506.
109. Zhao, X., Demary, K., Wong, L., Vaziri, C., Mckenzie, A.B., Eberlein, T.J. Spanjaard, R.A. (2001). Retinoic acid receptor-independent mechanism of apoptosis of melanoma cells by the retinoid CD437 (AHPN). Cell Death Differ., 8, 878 886.
110. Zuidervaart, W., Van Der Velden, P.A., Hurks, M.H., Van Nieuwpoort, F.A., Out-Luiting, C.J., Singh, A.D., Frants, R.R., Jager, M.J. Gruis, N.A. (2003). Gene expression profiling identifies tumour markers potentially playing a role in uveal melanoma development. Br. J. Cancer, 89, 1914 1919.