JOURNAL BROWSE
Search
Advanced SearchSearch Tips
Gene Set Analysis - Absolute and Trim
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
Gene Set Analysis - Absolute and Trim
Lee, Kwang-Hyun; Lee, Sun-Ho;
  PDF(new window)
 Abstract
Initial work of microarray data analysis focused on identification of differentially expressed genes, and recently, the focus has moved to discovering significant sets of functionally related genes. We describe some problems of GSEA and PAGE, and propose a modified method to identify significant gene sets. The results based on a simulated experiment and real data analysis using a set of publicly available data show the superiority of the newly proposed method, GSA-AT, in detecting significant pathways with the accurate prediction.
 Keywords
Microarray;gene-set;PAGE;GSEA;GSA-AT;
 Language
Korean
 Cited by
1.
마이크로어레이 자료분석에서 모수적 방법을 이용한 유전자군의 유의성 검정,이선호;이승규;이광현;

Communications for Statistical Applications and Methods, 2009. vol.16. 3, pp.397-408 crossref(new window)
 References
1.
Curtis, R. K., Oresic, M., Vidal-Puig, A. (2005). Pathways to the analysis of microarray data, Trend in Biotechnology, 23, 429-435 crossref(new window)

2.
Goeman, J. J., van de Geer, S. A., de Kort, F., van Houwelingen, H. C. (2004). A global test for groups of genes: Testing association with a clinical outcome, Bioinformatics, 20, 93-99 crossref(new window)

3.
Kim, S. Y. and Volsky, D. J. (2005). PAGE: Parametric analysis of gene set enrichment, BMC Bioinformatics, 6, 1471-2105

4.
Manoli, T., Gretz, N., Grone, H. J., Kenzelmann, M., Eils, R. and Brors, B. (2006). Group testing for pathway analysis improves comparability of different microarray datasets, Bioinformatics, 22, 2500-2506 crossref(new window)

5.
Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E., Houstis, N., Daly, M. J., Patterson, N., Mesirov, J. P., Golub, T. R., Tamayo, P., Spiegelman, B., Lander, E. S., Hirschhorn, J. N., Altshuler, D. and Groop, L. C. (2003). PGC-1 alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes, Nature Genetics, 34, 267-273. crossref(new window)

6.
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. and Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. In Proceedings of the National Academy of Sciences of the United States of America, 102, 15545-15550

7.
Tibshirani, R., Hastie, T., Narasimhan, B. and Chu, G. (2002). Diagnosis of multiple cancer types by shrunken centroids of gene expression, In Proceedings of the National Academy of Sciences of the United States of America, 99, 6567-6572

8.
Tusher, V. G., Tibshirani, R. and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response, In Proceedings of the National Academy of Sciences of the United States of America, 98, 5116-5121