Skip Navigation

Bioinformatics 2005 21(20):3859-3864; doi:10.1093/bioinformatics/bti549
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Alert me when this article is cited
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 (7)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Willbrand, K.
Right arrow Articles by Fink, T. M. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Willbrand, K.
Right arrow Articles by Fink, T. M. A.
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}oxfordjournals.org

Identifying genes from up–down properties of microarray expression series

Karen Willbrand 1, Francois Radvanyi 2, Jean-Pierre Nadal 1, Jean-Paul Thiery 2 and Thomas M. A. Fink 2,3,*

1Laboratoire de Physique Statistique Ecole Normale Supérieure, 75231 Paris Cedex 05, France
2Institut Curie CNRS UMR 144, Paris, 75248 France
3Theory of Condensed Matter, Cavendish Laboratory Cambridge CB3 0HE, UK

*To whom correspondence should be addressed.

Motivation: We consider any collection of microarrays that can be ordered to form a progression; for example, as a function of time, severity of disease or dose of a stimulant. By plotting the expression level of each gene as a function of time, or severity, or dose, we form an expression series, or curve, for each gene. While most of these curves will exhibit random fluctuations, some will contain a pattern, and these are the genes that are most likely associated with the quantity used to order them.

Results: We introduce a method of identifying the pattern and hence genes in microarray expression curves without knowing what kind of pattern to look for. Key to our approach is the sequence of ups and downs formed by pairs of consecutive data points in each curve. As a benchmark, we blindly identified genes from yeast cell cycles without selecting for periodic or any other anticipated behaviour.

Contact: tmf20{at}cam.ac.uk

Supplementary information: The complete versions of Table 2 and Figure 4, as well as other material, can be found at http://www.lps.ens.fr/~willbran/up-down/ or http://www.tcm.phy.cam.ac.uk/~tmf20/up-down/

Received on February 1, 2005; revised on May 2, 2005; accepted on June 16, 2005

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
 Nucleic Acids ResHome page
N. P. Gauthier, M. E. Larsen, R. Wernersson, U. de Lichtenberg, L. J. Jensen, S. Brunak, and T. S. Jensen
Cyclebase.org a comprehensive multi-organism online database of cell-cycle experiments
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D854 - D859.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Sahoo, D. L. Dill, R. Tibshirani, and S. K. Plevritis
Extracting binary signals from microarray time-course data
Nucleic Acids Res., June 28, 2007; 35(11): 3705 - 3712.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. E. Ahnert, K. Willbrand, F. C. S. Brown, and T. M. A. Fink
Unbiased pattern detection in microarray data series
Bioinformatics, June 15, 2006; 22(12): 1471 - 1476.
[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.