Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes.
In mammals, circadian periodicity has been described for gene expression in the hypothalamus and multiple peripheral tissues. It is accepted that 10%-15% of all genes oscillate in a daily rhythm, regulated by an intrinsic molecular clock. Statistical analyses of periodicity are limited by the small size of datasets and high levels of stochastic noise. Here, we propose a new approach applying digital signal processing algorithms separately to each group of genes oscillating in the same phase. Combined with the statistical tests for periodicity, this method identifies circadian baseline oscillation in almost 100% of all expressed genes. Consequently, circadian oscillation in gene expression should be evaluated in any study related to biological pathways. Changes in gene expression caused by mutations or regulation of environmental factors (such as photic stimuli or feeding) should be considered in the context of changes in the amplitude and phase of genetic oscillations.
Ptitsyn
Andrey A
AA
Department of Microbiology, Immunology and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America. Andrey.Ptitsyn@colostate.edu
Zvonic
Sanjin
S
Gimble
Jeffrey M
JM
D000818:Animals; D001683:Biological Clocks / Q000502:physiology*; D002940:Circadian Rhythm / Q000502:physiology*; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000502:physiology*; D006801:Humans; D008322:Mammals; D008954:Models, Biological; D010363:Pattern Recognition, Automated / Q000379:methods; D020543:Proteome / Q000235:genetics* / Q000378:metabolism*; D012815:Signal Processing, Computer-Assisted
D020543:Proteome