Prediction of gene function by genome-scale expression analysis: Prostate cancer-associated genes

Genome Research

Volumn 9, Issue 12, 1999, Pages 1198-1203

  Walker, Michael G ^a,b   Volkmuth, Wayne ^a   Sprinzak, Einat ^a   Hodgson, David ^a   Klingler, Tod ^a  

^a Experimental Station   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA LIBRARY; GENE EXPRESSION; GENE FUNCTION; HUMAN; PREDICTION; PRIORITY JOURNAL; PROSTATE CANCER;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MALE; MOLECULAR SEQUENCE DATA; PROSTATIC NEOPLASMS; PROTO-ONCOGENE PROTEINS;

EUKARYOTA;

EID: 0033452362     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.9.12.1198     Document Type: Article

References (42)

1. Agresti, A. 1990. Categorical data analysis. Wiley, New York, NY.
2. Bostwick, D. 1998. Pathology of prostate cancer. In Prostate cancer, (ed. M. Ernstoff, J. Heaney, and R. Peschel), pp. 15. Blackwell Science, Malden, MA.
3. Charlesworth, M.C., C.Y. Young, G.G. Klee, M.S. Saedi, S.D. Mikolajczyk, J.A. Finlay, and D.J. Tindall. 1997. Detection of a prostate-specific protein, human glandular kallikrein (hK2), in sera of patients with elevated prostate-specific antigen levels. Urology 49: 487-493.
4. Corey, E., K.R. Buhler, and R.L. Vessella. 1997. Cross-reactivity of ten anti-prostate-specific antigen monoclonal antibodies with human glandular kallikrein. Urology 50: 567-571.
5. Cramer, S., E. Blind, and D. Peehl. 1998. Detection of prostate specific antigen (PSA)-cleaved parathyroid hormone-related protein (PTHrP) in human serum. Proc. Am. Assoc. Cancer Res. 39: 105.
6. DeRisi, J., L. Penland, P.O. Brown, M.L. Bittner, P.S. Meltzer, M. Ray, Y. Chen, Y.A. Su, and J.M. Trent. 1996. Use of a cDNA microarray to analyze gene expression patterns in human cancer. Nat. Genet. 14: 457-460.
7. Dubbink, H.J., N.S. Verkaik, P.W. Faber, J. Trapman, F.H. Schroder, and J.C. Romijn. 1996. Tissue specific and androgen-regulated expression of human prostate-specific transglutaminase. Biochem. J. 315: 901-908.
8. Eerola, R., T. Piironen, K. Pettersson, J. Lovgren, M. Vehniainen, H. Lilja, B. Dowell, T. Lovgren, and M. Karp. 1997. Immunoreactivity of recombinant human glandular kallikrein using monoclonal antibodies raised against prostate-specific antigen. Prostate 31: 84-90.
9. Eisen, M.B., P.T. Spellman, P.O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863-14868.
10. Fannon, M.R. 1996. Gene expression in normal and disease states - identification of therapeutic targets. Trends Biotechnol. 14: 294-298.
11. Foster, H. 1998. Diagnostic evaluation of prostate cancer. In Prostate cancer, (ed. M. Ernstoff, J. Heaney, and R. Peschel), pp. 48. Blackwell Science, Malden, MA.
12. Freije, J.P., A. Fueyo, J.A. Uria, G. Velasco, L.M. Sanchez, Y.S. Lopez-Boado, and C. Lopez-Otin. 1993 Human Zn-alpha 2-glycoprotein: Complete genomic sequence, identification of a related pseudogene and relationship to class I major histocompatibility complex genes. Genomics 18: 575-587.
13. Gagnon, S., B. Tetu, J.Y. Dube, and R.R. Tremblay. 1990. Expression of Zn-alpha 2-glycoprotein and PSP-94 in prostatic adenocarcinoma. An immunohistochemical study of 88 cases. Am. J. Pathol. 136: 1147-1152.
14. Greller, L.D. and F.L. Tobin. 1999. Detecting selective expression of genes and proteins. Genome Res. 9: 282-296.
15. Guo, Y. and N. Kyprianou. 1998. Overexpression of transforming growth factor (TGF) beta1 type II receptor restores TGF-beta1 sensitivity and signaling in human prostate cancer cells. Cell Growth Differ. 9: 185-193.
16. Hurlimann, J. and G. van Melle. 1991. Prognostic value of serum proteins synthesized by breast carcinoma cells. Am. J. Clin. Pathol. 95: 835-843.
17. Lashkari, D.A., J.L. DeRisi, J.H. McCusker, A.F. Namath, C. Gentile, S.Y. Hwang, P.O. Brown, and R.W. Davis. 1997. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. 94: 13057-13062.
18. Lockhart, D.J., H. Dong, M.C. Byrne, M.T. Follettie, M.V. Gallo, M.S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton et al. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays [In Process Citation]. Nat. Biotechnol. 14: 1675-1680.
19. Lopez-Boado, Y.S., I. Diez-Itza, J. Tolivia, and C. Lopez-Otin. 1994. Glucocorticoids and androgens up-regulate the Zn-alpha 2-glycoprotein messenger RNA in human breast cancer cells. Breast Cancer Res. Treat. 29: 247-258.
20. Mack, D., G.W. Hacker, C. Hauser-Kronberger, J. Frick, and O. Dietze. 1997. Vasoactive intestinal polypeptide (VIP) and neuropeptide tyrosine (NPY) in prostate carcinoma. Eur. J. Cancer. 33: 317-318.
21. Mbikay, M., S. Nolet, S. Fournier, S. Benjannet, P. Chapdelaine, G. Paradis, J.Y. Dube, R. Tremblay, C. Lazure, N.G. Seidah et al. 1987. Molecular cloning and sequence of the cDNA for a 94-amino-acid seminal plasma protein secreted by the human prostate. DNA 6: 23-29.
22. Michaels, G.S., D.B. Carr, S. Fuhrman, X. Wen, and R. Somogyi. 1998. Cluster analysis and data visualization of large-scale gene expression data. In Pacific symposium on biocomputing, (ed. R. Altman, A. Dunker, L. Hunter, and T. Klein), pp. 42. World Scientific, Singapore.
23. Mikolajczyk, S.D., L.S. Millar, A. Kumar, and M.S. Saedi. 1998. Human glandular kallikrein, hK2, shows arginine-restricted specificity and forms complexes with plasma protease inhibitors. Prostate 34: 44-50.
24. Minth, C.D., S.R. Bloom, J.M. Polak, and J.E. Dixon. 1984. Cloning, characterization, and DNA sequence of a human cDNA encoding neuropeptide tyrosine. Proc. Natl. Acad. Sci. 81: 4577-4581.
25. Morris, D.L., P.W. Dillon, D.L. Very, P. Ng, L. Kish, J.L. Goldblatt, D.J. Bruzek, D.W. Chan, M.S. Ahmed, D. Witek et al. 1998. Bayer Immuno 1 PSA Assay: An automated, ultrasensitive method to quantitate total PSA in serum. J. Clin. Lab. Anal. 12: 65-74.
26. Morrison, B.W., J.R. Moorman, G.C. Kowdley, Y.M. Kobayashi, L.R. Jones, and P. Leder. 1995. Mat-8, a novel phospholemman-like protein expressed in human breast tumors, induces a chloride conductance in Xenopus oocytes. J. Biol. Chem. 270: 2176-2182.
27. Nelson, P.S., L. Gan, C. Ferguson, P. Moss, R. Gelinas, L. Hood, and K. Wang. 1999. Molecular cloning and characterization of prostase, an androgen-regulated serine protease with prostate-restricted expression. Proc. Natl. Acad. Sci. 96: 3114-3119.
28. Pant, N., A.K. Prasad, S.C. Srivastava, R. Shankar, and S.P. Srivastava. 1995. Effect of oral administration of carbofuran on male reproductive system of rat. Hum. Exp. Toxicol. 14: 889-894.
29. Parker, S.L., T. Tong, S. Bolden, and P.A. Wingo. 1996. Cancer statistics, 1996. CA Cancer J. Clin. 46: 5-27.
30. Perry, K.T., C.T. Anthony, T. Case, and M.S. Steiner. 1997. Transforming growth factor beta as a clinical biomarker for prostate cancer. Urology 49: 151-155.
31. Presti, J.C., Jr. and P.R. Carroll. 1996. Use of prostate-specific antigen (PSA) and PSA density in the detection of stage T1 carcinoma of the prostate. Semin. Urol. Oncol. 14: 134-138.
32. Presti, J., M. Stoller, and P. Carroll. 1996. Urology. In Current medical diagnosis and treatment, (ed. L. Tierney, S. McPhee, and M. Papadakis), pp. 822-857. Lange, Stamford, CT.
33. Rentzepis, M., P. Gumerlock, and R. deVere White. 1998. Future directions in prostate cancer research. In Prostate cancer, (ed. M. Ernstoff, J. Heaney, and R. Peschel), pp. 203-209. Blackwell Science, Malden, MA.
34. Richie, J. and I. Kaplan. 1996. Screening for prostate cancer: The horns of a dilemma. In Prostate cancer: A multidisciplinary guide, (ed. P. Kantoff, K. Wishnow, and K. Loughlin), pp. 1-10. Blackwell Science, Malden, MA.
35. Schiemann, S., M. Schwirzke, N. Brunner, and U.H. Weidle. 1998. Molecular analysis of two mammary carcinoma cell lines at the transcriptional level as a model system for progression of breast cancer. Clin. Exp. Metastasis 16: 129-139.
36. Stamey, T.A. 1996. Lower limits of detection, biological detection limits, functional sensitivity, or residual cancer detection limit? Sensitivity reports on prostate-specific antigen assays mislead clinicians. Clin. Chem. 42: 849-852.
37. Tamayo, P., D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E.S. Lander, and T.R. Golub et al. 1999. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. 96: 2907-2912.
38. Thomas, T.Z., S.M. Chapman, W. Hong, C. Gurusingfhe, S.L. Mellor, R. Fletcher, J. Pedersen, and G.P. Risbridger. 1998. Inhibins, activins, and follistatins: Expression of mRNAs and cellular localization in tissues from men with benign prostatic hyperplasia. Prostate 34: 34-43.
39. Vasmatzis, G., M. Essand, U. Brinkmann, B. Lee, and I. Pastan. 1998. Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis. Proc. Natl. Acad. Sci. 95: 300-304.
40. Wen, X., S. Fuhrman, G.S. Michaels, D.B. Carr, S. Smith, J.L. Barker, and R. Somogyi. 1998. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl. Acad Sci. 95: 334-339.
41. Whittemore, A.S., C. Lele, G.D. Friedman, T. Stamey, J.H. Vogelman, and N. Orentreich. 1995. Prostate-specific antigen as predictor of prostate cancer in black men and white men. J. Natl. Cancer Inst. 87: 354-360.
42. Zhang, L., W. Zhou, V.E. Velculescu, S.E. Kern, R.H. Hruban, S.R. Hamilton, B. Vogelstein, and K.W. Kinzler. 1997. Gene expression profiles in normal and cancer cells. Science 276: 1268-1272.