Skip Navigation



Bioinformatics Advance Access published online on April 15, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth274
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
20/16/2521    most recent
bth274v1
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 Liu, D.
Right arrow Articles by Peddada, S. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Liu, D.
Right arrow Articles by Peddada, S. D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received February 13, 2004
Revised March 24, 2004
Accepted March 26, 2004

Article

A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions

Delong Liu 1, Clarice R. Weinberg 1, Shyamal D. Peddada 1*

1 Biostatistics Branch, MD:A3-03, National Institute of Environmental Health Sciences, National Institutes of Health, P.O.Box 12233, Research Triangle Park, NC 27709

* To whom correspondence should be addressed. E-mail: peddada{at}niehs.nih.gov.


  Abstract

Differing arresting agents and protocols can be used to synchronize cells in cultures to specific phases of the cell when studying cell cycle gene expressions. Often, data derived from individual experiments are analyzed separately, since no appropriate statistical methodology is available at the moment to analyze the data from all such experiments simultaneously. The focus of this paper is to determine the association and coherence of the relative activation times of cell-cycling genes under different experimental conditions. Using the circular-circular regression model of Downs and Mardia (2002), we define two parameters, a rotation parameter for the angular difference between cells' arresting times (phases) in two cell cycle experiments, and an association parameter to describe the correspondence between the cycle times of maximal expression (phase angles) for a set of genes studied in two experiments. Further, we propose a procedure to assess coherence across multiple experiments, that is, to what extent the circular ordering of the phase angles of genes is maintained across multiple experiments. Coherence of genes across experiments suggests that functionally these genes tend to respond in a stereotypically sequenced way under different experimental conditions. Our proposed methodology is illustrated by applying it to the HeLa cell cycle gene expression data described in Whitfield et al. (2002).


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




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.