Abstract
Most oncological microarray studies focus on molecular distinctions in different cancer entities. Recently, researchers started using microarrays for investigating molecular commonalities of multiple cancer types. This poses novel bioinformatics challenges.
In this paper we describe a method that detects common molecular mechanisms in different cancer entities. The method extends previously described concepts by introducing Meta-Analysis Pattern Matches. In an analysis of four prognostic cancer studies, involving breast cancer, leukemia, and mesothelioma, we are able to identify 42 genes that show consistent up- or down-regulation in patients with a poor disease outcome. These genes complement the set of previously published candidates for universal prognostic markers in cancer.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Affymetrix: 2001a, Microarray suite user guide, version 5.0.
A. Alizadeh, M. Eisen, R. Davis, C. Ma, I. Losses, A. Rosenwald, et al., Nature 403, 503 (2000).
S. Bandyopadhyay, S. Pai, S. Gross, S. Hirota, S. Hosobe, K. Miura, K. Saito, T. Commes, S. Hayashi, M. Watabe, and K. Watabe, Cancer Res 63(8), 1731 (2003).
D. Bennin, A. Don, T. Brake, J. McKenzie, H. Rosen-baum, L. Ortiz, A. DePaoli-Roach, and M. Horne, J Biol Chem 277(30), 27449 (2002).
S. Chiaretti, X. Li, R. Gentleman, A. Vitale, M. Vignetti, F. Mandelli, J. Ritz, and R. Foa, Blood 103(7), 2771 (2004).
S. Ghosh, M. May, and E. Kopp, Annu Rev Immunol 16, 225 (1998).
G. Gordon, R. Jensen, L. Hsiao, S. Gullans, J. Blumenstock, W. Richards, M. Jaklitsch, D. Sugarbaker, and R. Bueno, Journal of the National Cancer Institute 95(8), 598 (2003).
J. Harper, J. Yuan, J. Tan, I. Visan, and C. Guidos, Clin Genet 64(6), 461 (2003).
E. Huang, S. Cheng, H. Dressman, J. Pittman, M. Tsou, C. Horng, A. Bild, E. Iversen, M.L. M, C. Chen, M.W. M, J. Nevins, and A. Huang, Lancet. 361(9369), 1590 (2003).
W. Huber, A. von Heydebreck, H. Sueltmann, A. Poustka, and M. Vingron, Bioinformatics 18 Suppl 1, 96 (2002).
R. Irizarry, B. Hobbs, F. Collin, Y. Beazer-Barclay, K. Antonellis, U. Scherf, and T. Speed, Bio-statistics 4(2), 249 (2003).
J. Kuai, E. Nickbarg, J. Wooters, Y. Qiu, J. Wang, and L. Lin, J Biol Chem 278(16), 14363 (2003).
C. Lin, A. Lau, C. Yeh, C. Chang, and T. Lue, DNA Cell Biol 19(1), 1 (2000).
E. Moon and A. Lerner, Blood 101(10), 4122 (2003).
A. Rao, C. Luo, and P. Hogan, Annu Rev Immunol 15, 707 (1997).
D. Rhodes, J. Yu, K. Shanker, N. Deshpande, R. Varambally, D. Ghosh, T. Barrette, A. Pandey, and A. Chinnaiyan, Proc Natl Acad Sci USA 101(25), 9309 (2004).
E. Segal, N. Friedman, D. Koller, and A. Regev, Nature Genetics 36(10), 1090 (2004).
H. Shimada, Y. Nabeya, S. Okazumi, H. Matsubara, K. Kadomatsu, T. Muramatsu, S. Ikematsu, S. Sakuma, and T. Ochiai, Oncol Rep 10(2), 411 (2003).
M. Smid and C.L.D.G. Jenster, Bioinformatics 19(16), 2065 (2003).
M. West, C. Blanchette, H. Dressman, E. Huang, S. Ishida, R. Spang, et al., Proc. Natl. Acad. Sci. USA 98, 11462 (2001).
E. Yeoh, M. Ross, S. Shurtleff, W. Williams, D. Patel, R. Mahfouz, P. Behm, et al., Cancer Cell 1(2), 133 (2002).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Yang, X., Bentink, S. & Spang, R. Detecting Common Gene Expression Patterns in Multiple Cancer Outcome Entities. Biomed Microdevices 7, 247–251 (2005). https://doi.org/10.1007/s10544-005-3032-7
Issue Date:
DOI: https://doi.org/10.1007/s10544-005-3032-7