Abstract
Circadian oscillation in baseline gene expression plays an important role in the regulation of multiple cellular processes. Most of the knowledge of circadian gene expression is based on studies measuring gene expression over time. Our ability to dissect molecular events in time is determined by the sampling frequency of such experiments. However, the real peaks of gene activity can be at any time on or between the time points at which samples are collected. Thus, some genes with a peak activity near the observation point have their phase of oscillation detected with better precision then those which peak between observation time points. Separating genes for which we can confidently identify peak activity from ambiguous genes can improve the analysis of time series gene expression. In this study we propose a new statistical method to quantify the phase confidence of circadian genes. The numerical performance of the proposed method has been tested using three real gene expression data sets.
Highlights
Analysis of periodic patterns is an essential part of many studies of gene expression involving timeline sampling or targeting of rhythmically expressed genes
The data are derived from microarray study of gene expression in three tissues in mice referred as Inguinal White Adipose tissue (IWAT), Brown Adipose Tissue (BAT) and Liver
Each profile consists of 12 time points of 4-h interval difference
Summary
Analysis of periodic patterns is an essential part of many studies of gene expression involving timeline sampling or targeting of rhythmically expressed genes. The absolute amplitude and time of the peak (i.e. phase) of rhythmic gene expression are analyzed and reported. It has been observed that low sampling frequency presents a significant challenge to all studies of periodic gene expression ([7] for review). Most gene expression studies only report 6 or 9 observation points per period and not more than two consecutive periods in the entire timeline. Some oscillating genes may have peak expression coinciding at, or near, the observation point (i.e. the time when the animal is sacrificed and tissue samples are taken for analysis). Other genes may peak at any time between sparsely placed observations. Since our ability to differentiate events in time is restricted by the low PLOS ONE | DOI:10.1371/journal.pone.0131111 July 10, 2015
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