Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2016, Article ID 3017475, 14 pages
http://dx.doi.org/10.1155/2016/3017475
Research Article

Finding Clocks in Genes: A Bayesian Approach to Estimate Periodicity

1Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267-0056, USA
2Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267-0576, USA
3Department of Mathematical Sciences, University of Cincinnati, Cincinnati, OH 45221-0025, USA

Received 3 November 2015; Accepted 28 April 2016

Academic Editor: Sher Afzal Khan

Copyright © 2016 Yan Ren et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Identification of rhythmic gene expression from metabolic cycles to circadian rhythms is crucial for understanding the gene regulatory networks and functions of these biological processes. Recently, two algorithms, JTK_CYCLE and ARSER, have been developed to estimate periodicity of rhythmic gene expression. JTK_CYCLE performs well for long or less noisy time series, while ARSER performs well for detecting a single rhythmic category. However, observing gene expression at high temporal resolution is not always feasible, and many scientists are interested in exploring both ultradian and circadian rhythmic categories simultaneously. In this paper, a new algorithm, named autoregressive Bayesian spectral regression (ABSR), is proposed. It estimates the period of time-course experimental data and classifies gene expression profiles into multiple rhythmic categories simultaneously. Through the simulation studies, it is shown that ABSR substantially improves the accuracy of periodicity estimation and clustering of rhythmic categories as compared to JTK_CYCLE and ARSER for the data with low temporal resolution. Moreover, ABSR is insensitive to rhythmic patterns. This new scheme is applied to existing time-course mouse liver data to estimate period of rhythms and classify the genes into ultradian, circadian, and arrhythmic categories. It is observed that 49.2% of the circadian profiles detected by JTK_CYCLE with 1-hour resolution are also detected by ABSR with only 4-hour resolution.