Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data.
Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data.
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DOI：
10.1038/s41598-018-26735-4
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发表时间：
2018-05-29
影响因子：
4.6
通讯作者：
Nagano AJ
中科院分区：
文献类型：
--
作者：
Awazu A;Tanabe T;Kamitani M;Tezuka A;Nagano AJ
在相同的环境条件下，基因表达水平在遗传上相同的生物体中表现出随机变化。在许多最近的基于RNA测序（RNA-seq）的转录组分析中，假设重复之间基因表达水平的变化遵循负二项分布，尽管这种假设的生理基础尚不清楚。在这项研究中，RNA-seq数据获得了拟南芥在8个条件下（21-27重复），并分析了基因依赖的经验概率密度函数（ePDF）的基因表达水平的轮廓的特点。对于. thaliana和Saccharomyces cerevisiae中，获得了各种类型的基因表达水平的ePDF，其被分类为高斯型、含有长尾的幂律型或中间型。这些ePDF配置文件与高斯幂混合分布函数很好地拟合，该分布函数来自包含反馈环的随机转录网络的简单模型。拟合函数表明，具有长尾ePDF的基因表达水平将受到反馈调节的强烈影响。此外，基因表达水平的特征与它们的功能相关，必需基因的水平倾向于遵循高斯样ePDF，而编码核酸结合蛋白和转录因子的基因的水平表现出长尾ePDF。
Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution, although the physiological basis of this assumption remains unclear. In this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21–27 replicates), and the characteristics of gene-dependent empirical probability density function (ePDF) profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, various types of ePDF of gene expression levels were obtained that were classified as Gaussian, power law-like containing a long tail, or intermediate. These ePDF profiles were well fitted with a Gauss-power mixing distribution function derived from a simple model of a stochastic transcriptional network containing a feedback loop. The fitting function suggested that gene expression levels with long-tailed ePDFs would be strongly influenced by feedback regulation. Furthermore, the features of gene expression levels are correlated with their functions, with the levels of essential genes tending to follow a Gaussian-like ePDF while those of genes encoding nucleic acid-binding proteins and transcription factors exhibit long-tailed ePDF.
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影响因子：
64.5
作者：
Mitsui, K;Tokuzawa, Y;Yamanaka, S
通讯作者：
Yamanaka, S
DOI：
10.2142/biophysics.1.25
发表时间：
2005
期刊：
Biophysics (Nagoya-shi, Japan)
影响因子：
--
作者：
Furusawa C;Suzuki T;Kashiwagi A;Yomo T;Kaneko K
通讯作者：
Kaneko K
影响因子：
56.9
作者：
Landry, Christian R.;Lemos, Bernardo;Hartl, Daniel L.
通讯作者：
Hartl, Daniel L.
影响因子：
3.7
作者：
Konishi, Tomokazu;Konishi, Fumikazu;Konagaya, Akihiko
通讯作者：
Konagaya, Akihiko
影响因子：
64.8
作者：
Chang, Hannah H.;Hemberg, Martin;Huang, Sui
通讯作者：
Huang, Sui