Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes.
Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes.
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DOI：
10.1371/journal.pcbi.0030120
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发表时间：
2007-06
影响因子：
4.3
通讯作者：
Gimble, Jeffrey M.
中科院分区：
文献类型：
--
作者：
Ptitsyn, Andrey A.;Zvonic, Sanjin;Gimble, Jeffrey M.
在哺乳动物中，已经描述了下丘脑和多种外周组织中基因表达的昼夜节律周期性。人们普遍认为，10%-15%的基因以每天的节奏振荡，由内在的分子钟调节。周期性的统计分析受到数据集规模小和随机噪声水平高的限制。在这里，我们提出了一种新的方法，分别应用数字信号处理算法的每一组基因在同一相位振荡。结合周期性的统计检验，该方法几乎100%地识别了所有表达基因的昼夜节律基线振荡。因此，基因表达的昼夜节律振荡应该在任何与生物学途径相关的研究中进行评估。由突变或环境因素（如光刺激或喂养）的调节引起的基因表达的变化应在遗传振荡的幅度和相位变化的背景下考虑。先前的研究已经报道，约15%的表达基因显示与特定功能相关的昼夜表达模式。一系列的实验和计算研究的基因表达在不同的小鼠组织，使我们得出了不同的结论。通过应用一种新的分析策略和一些替代算法，我们确定了几乎100%的基因的基线振荡。虽然振荡的相位和幅度在不同的组织之间存在差异，但昼夜节律振荡仍然是每个基因的基本特性。对先前发表的数据的重新分析也揭示了比先前报道的更多的振荡基因。这表明昼夜节律振荡是所有哺乳动物基因的普遍属性，尽管振荡的相位和振幅是组织特异性的，并且仍然与基因的功能相关。我们假设细胞的代谢呼吸周期驱动基因表达的振荡模式。这些发现意味着，生物途径应被视为相互协调的基因振荡的动态系统。
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. Prior studies have reported that ~15% of expressed genes show a circadian expression pattern in association with a specific function. A series of experimental and computational studies of gene expression in various murine tissues has led us to a different conclusion. By applying a new analysis strategy and a number of alternative algorithms, we identify baseline oscillation in almost 100% of all genes. While the phase and amplitude of oscillation vary between different tissues, circadian oscillation remains a fundamental property of every gene. Reanalysis of previously published data also reveals a greater number of oscillating genes than was previously reported. This suggests that circadian oscillation is a universal property of all mammalian genes, although phase and amplitude of oscillation are tissue-specific and remain associated with a gene's function. We hypothesize that the cell's metabolic respiratory cycle drives the oscillatory pattern of gene expression. These findings imply that biological pathways should be considered as dynamic systems of genes oscillating in coordination with each other.
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影响因子：
4.3
作者：
Ptitsyn, Andrey A;Zvonic, Sanjin;Conrad, Steven A;Scott, L Keith;Mynatt, Randall L;Gimble, Jeffrey M
通讯作者：
Gimble, Jeffrey M
DOI：
10.1111/j.1533-869x.2003.01097.x
发表时间：
2003-09-01
影响因子：
--
作者：
Halberg, Franz;Cornelissen, Germaine;Governor Shri Vishnu Kant Shastri
通讯作者：
Governor Shri Vishnu Kant Shastri
DOI：
10.1073/pnas.0306490101
发表时间：
2004-02-03
影响因子：
11.1
作者：
Klevecz, RR;Bolen, J;Murray, DB
通讯作者：
Murray, DB
DOI：
10.1111/j.1432-1033.1968.tb00175.x
发表时间：
1968-01-01
期刊：
EUROPEAN JOURNAL OF BIOCHEMISTRY
影响因子：
--
作者：
SELKOV, EE
通讯作者：
SELKOV, EE
影响因子：
3
作者：
Ptitsyn AA;Zvonic S;Gimble JM
通讯作者：
Gimble JM