Skip Navigation



Bioinformatics Advance Access published online on August 4, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti592
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/17/3524    most recent
bti592v1
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Hu, J.
Right arrow Articles by Coombes, K. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hu, J.
Right arrow Articles by Coombes, K. R.
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@oupjournals.org
Received February 7, 2005
Revised May 22, 2005
Accepted July 18, 2005

Article

Analysis of dose-response effects on gene expression data with comparison of two microarray platforms

Jianhua Hu 1, Mini Kapoor 2, Wei Zhang 3, Stanley R. Hamilton 3, and Kevin R. Coombes 1*

1 Department of Biostatistics and Applied Mathematics, University of Texas M.D. Anderson Cancer Center 77030, USA
2 Department of Cancer Genetics, University of Texas M.D. Anderson Cancer Center 77030, USA
3 Department of Pathology, University of Texas M.D. Anderson Cancer Center 77030, USA

* To whom correspondence should be addressed.
Kevin R. Coombes, E-mail: kcoombes{at}mdanderson.org


  Abstract

Motivation: The problems of analyzing dose effects on gene expression are gaining attention in biomedical research. A particular challenge is to detect genes with expression levels that change according to dose levels in a nonrandom manner, but nonetheless may be considered as potential biomarkers.

Method: We are among the first to formally apply a tool that uses an isotonic (monotonic) regression approach to this area of study. We introduce a test statistic to select genes with significant dose-response expression in a monotonic fashion based on a permutation procedure. We then compare the results to those achieved from the application of a likelihood ratio-based test.

Results: We apply the isotonic regression approach to a study of gene expression in the RKO colon Carcinoma cell line in response to varying dosage levels of the chemotherapeutic agent 5-fluorouracil (5-FU). A feature of both Affymetrix and printed 75mer oligomer cDNA arrays produced from the same samples provides an opportunity to compare the two microarray platforms.

Availability: Statistical software S-plus Code to implement the method is available from the authors.


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
 Cancer Prevention ResearchHome page
H. Kadara, L. Lacroix, C. Behrens, L. Solis, X. Gu, J. J. Lee, E. Tahara, D. Lotan, W. K. Hong, I. I. Wistuba, et al.
Identification of Gene Signatures and Molecular Markers for Human Lung Cancer Prognosis using an In vitro Lung Carcinogenesis System
Cancer Prevention Research, August 1, 2009; 2(8): 702 - 711.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. L. Brigand, R. Russell, C. Moreilhon, J.-M. Rouillard, B. Jost, F. Amiot, V. Magnone, C. Bole-Feysot, P. Rostagno, V. Virolle, et al.
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes
Nucleic Acids Res., July 19, 2006; 34(12): e87 - e87.
[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.