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Nucleic Acids Research Advance Access originally published online on May 21, 2007
Nucleic Acids Research 2007 35(11):3705-3712; doi:10.1093/nar/gkm284
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Nucleic Acids Research, 2007, Vol. 35, No. 11 3705-3712
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

Extracting binary signals from microarray time-course data

Debashis Sahoo1, David L. Dill2,*, Rob Tibshirani3 and Sylvia K. Plevritis4

1Department of Electrical Engineering, 2Department of Computer Science, 3Department of Radiology and 4Department of Health Research and Policy and Department of Statistics, Stanford University

*To whom correspondence should be addressed. Tel: +650 725 3642; Fax: +650 735 6949; Email: dill{at}cs.stanford.edu

Received November 29, 2006. Revised March 2, 2007. Accepted April 11, 2007.

This article presents a new method for analyzing microarray time courses by identifying genes that undergo abrupt transitions in expression level, and the time at which the transitions occur. The algorithm matches the sequence of expression levels for each gene against temporal patterns having one or two transitions between two expression levels. The algorithm reports a P-value for the matching pattern of each gene, and a global false discovery rate can also be computed. After matching, genes can be sorted by the direction and time of transitions. Genes can be partitioned into sets based on the direction and time of change for further analysis, such as comparison with Gene Ontology annotations or binding site motifs. The method is evaluated on simulated and actual time-course data. On microarray data for budding yeast, it is shown that the groups of genes that change in similar ways and at similar times have significant and relevant Gene Ontology annotations.


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