Bioinformatics 20(3) © Oxford University Press 2004; all rights reserved.
Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data
Rowe Program in Human Genetics, School of Medicine, University of California, Davis, CA 95616, USA
Received on April 10, 2003
; revised on June 27, 2003
; accepted on July 29, 2003
Motivation: The expressions of many genes associated with certain periodic biological and cell cycle processes such as circadian rhythm regulation are known to be rhythmic. Identification of the genes whose time course expressions are synchronized to certain periodic biological process may help to elucidate the molecular basis of many diseases, and these gene products may in turn represent drug targets relevant to those diseases.
Results: We propose in this paper a statistical framework based on a shape-invariant model together with a false discovery rate (FDR) procedure for identifying periodically expressed genes based on microarray time-course gene expression data and a set of known periodically expressed guide genes. We applied the proposed methods to the 
-factor, cdc15 and cdc28 synchronized yeast cell cycle data sets and identified a total of 1010 cell-cycle-regulated genes at a FDR of 0.5% in at least one of the three data sets analyzed, including 89 (86%) of 104 known periodic transcripts. We also identified 344 and 201 circadian rhythmic genes in vivo in mouse heart and liver tissues with FDR of 10 and 2.5%, respectively. Our results also indicate that the shape-invariant model fits the data well and provides estimate of the common shape function and the relative phases for these periodically regulated genes.
Availability: Matlab programs are available on request from the authors.
Supplementary information: http://dna.ucdavis.edu/~hli/period.html
Contact: hli{at}ucdavis.edu
* To whom correspondence should be addressed.
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