Skip Navigation


Bioinformatics Advance Access originally published online on January 18, 2005
Bioinformatics 2005 21(9):1950-1957; doi:10.1093/bioinformatics/bti267
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/9/1950    most recent
bti267v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (20)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Goeman, J. J.
Right arrow Articles by van Houwelingen, H. C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Goeman, J. J.
Right arrow Articles by van Houwelingen, H. C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Testing association of a pathway with survival using gene expression data

Jelle J. Goeman 1,2,*, Jan Oosting 3, Anne-Marie Cleton-Jansen 3, Jakob K. Anninga 4 and Hans C. van Houwelingen 1

1Department of Medical Statistics, Leiden University Medical Center PO Box 9604, 2300 RA Leiden, The Netherlands
2Mathematical Institute, Leiden University The Netherlands
3Department of Pathology, Leiden University Medical Center The Netherlands
4Department of Pediatrics, Leiden University Medical Center The Netherlands

*To whom correspondence should be addressed.

Motivation: A recent surge of interest in survival as the primary clinical endpoint of microarray studies has called for an extension of the Global Test methodology to survival.

Results: We present a score test for association of the expression profile of one or more groups of genes with a (possibly censored) survival time. Groups of genes may be pathways, areas of the genome, clusters from a cluster analysis or all genes on a chip. The test allows one to test hypotheses about the influence of these groups of genes on survival directly, without the intermediary of single gene testing. The test is based on the Cox proportional hazards model and is calculated using martingale residuals. It is possible to adjust the test for the presence of covariates. We also present a diagnostic graph to assist in the interpretation of the test result, visualizing the influence of genes. The test is applied to a tumor dataset, revealing pathways from the gene ontology database that are associated with survival of patients.

Availability: The Global Test for survival has been incorporated into the R-package globaltest (version 3.0), available at http://www.bioconductor.org

Contact: j.j.goeman{at}lumc.nl


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
I. Dinu, J. D. Potter, T. Mueller, Q. Liu, A. J. Adewale, G. S. Jhangri, G. Einecke, K. S. Famulski, P. Halloran, and Y. Yasui
Gene-set analysis and reduction
Brief Bioinform, January 1, 2009; 10(1): 24 - 34.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X. Chen, L. Wang, J. D. Smith, and B. Zhang
Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes
Bioinformatics, November 1, 2008; 24(21): 2474 - 2481.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
G. G. Van den Eynden, M. Smid, S. J. Van Laere, C. G. Colpaert, I. Van der Auwera, T. X. Bich, P. van Dam, M. A. den Bakker, L. Y. Dirix, E. A. Van Marck, et al.
Gene Expression Profiles Associated with the Presence of a Fibrotic Focus and the Growth Pattern in Lymph Node-Negative Breast Cancer
Clin. Cancer Res., May 15, 2008; 14(10): 2944 - 2952.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
D. Nam and S.-Y. Kim
Gene-set approach for expression pattern analysis
Brief Bioinform, May 1, 2008; 9(3): 189 - 197.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
M. Smid, Y. Wang, Y. Zhang, A. M. Sieuwerts, J. Yu, J. G.M. Klijn, J. A. Foekens, and J. W.M. Martens
Subtypes of Breast Cancer Show Preferential Site of Relapse
Cancer Res., May 1, 2008; 68(9): 3108 - 3114.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. J. Goeman and U. Mansmann
Multiple testing on the directed acyclic graph of gene ontology
Bioinformatics, February 15, 2008; 24(4): 537 - 544.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
F. Westermann, K.-O. Henrich, J. S. Wei, W. Lutz, M. Fischer, R. Konig, R. Wiedemeyer, V. Ehemann, B. Brors, K. Ernestus, et al.
High Skp2 Expression Characterizes High-Risk Neuroblastomas Independent of MYCN Status
Clin. Cancer Res., August 15, 2007; 13(16): 4695 - 4703.
[Abstract] [Full Text] [PDF]

Home page
 JCOHome page
D. Kienle, T. Katzenberger, G. Ott, D. Saupe, A. Benner, H. Kohlhammer, T. F.E. Barth, S. Holler, J. Kalla, A. Rosenwald, et al.
Quantitative Gene Expression Deregulation in Mantle-Cell Lymphoma: Correlation With Clinical and Biologic Factors
J. Clin. Oncol., July 1, 2007; 25(19): 2770 - 2777.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. M. Kemp, N. R. Nirmala, and J. D. Szustakowski
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation
Bioinformatics, June 1, 2007; 23(11): 1356 - 1362.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. J. Goeman and P. Buhlmann
Analyzing gene expression data in terms of gene sets: methodological issues
Bioinformatics, April 15, 2007; 23(8): 980 - 987.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. A. Zapala and N. J. Schork
Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables
PNAS, December 19, 2006; 103(51): 19430 - 19435.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.