Degree of Freedom of Gene Expression in Saccharomyces cerevisiae.
Degree of Freedom of Gene Expression in Saccharomyces cerevisiae.
复制标题
酿酒酵母基因表达的自由度
DOI：
10.1128/spectrum.00838-21
复制
发表时间：
2022-04-27
影响因子：
3.7
通讯作者：
He, Yungang
中科院分区：
文献类型：
--
作者：
Yang, Zhen;Xu, Feng;Xue, Aijuan;Lv, Hong;He, Yungang
由于缺乏全面的统计分析，全基因组基因表达的复杂性尚未得到充分解决。在本研究中，我们引入自由度(DOF)作为评估基因表达复杂性的综合统计量。摘要由于缺乏全面的统计分析，全基因组基因表达的复杂性尚未得到充分解决。在本研究中，我们引入自由度(DOF)作为评估基因表达复杂性的综合统计量。因为自由度可以用状态空间表示来解释，所以自由度的应用对于理解基因的活动是非常有用的。我们使用了超过11,000个基因表达数据集来揭示酿酒酵母中基因表达的DOF不大于450。我们进一步证明，不同程度的基因表达可以由启动子区域和基因本体论(GO)术语中的不同序列基序来解释。广为人知的TATA盒是已鉴定基序中最重要的一个，而GO术语“核糖体发生”是一个相关的生物学过程。在转录自由的基础上，我们的发现表明，基因表达的调节可以只使用几个状态变量来建模。重要酵母的运作就像一个组织良好的工厂。它的每个组件都以自己的方式工作，同时影响其他组件的活动。所有活动的顺序在很大程度上受基因表达调控的支配。近几十年来，生物学家已经认识到了酵母基因的许多规定。然而，目前尚不清楚该调控将每个基因紧密地联系在一起，使细胞的所有组成部分作为一个整体工作。换句话说，生物学家非常感兴趣的是，需要多少独立的控制因素才能运行一个与真实细胞工作相同的人造“细胞”。在这项工作中，我们认为只有450个控制因子足以代表所有5800个酵母基因的调控。
The complexity of genome-wide gene expression has not yet been adequately addressed due to a lack of comprehensive statistical analyses. In the present study, we introduce degree of freedom (DOF) as a summary statistic for evaluating gene expression complexity. ABSTRACT The complexity of genome-wide gene expression has not yet been adequately addressed due to a lack of comprehensive statistical analyses. In the present study, we introduce degree of freedom (DOF) as a summary statistic for evaluating gene expression complexity. Because DOF can be interpreted by a state-space representation, application of the DOF is highly useful for understanding gene activities. We used over 11,000 gene expression data sets to reveal that the DOF of gene expression in Saccharomyces cerevisiae is not greater than 450. We further demonstrated that various degrees of freedom of gene expression can be interpreted by different sequence motifs within promoter regions and Gene Ontology (GO) terms. The well-known TATA box is the most significant one among the identified motifs, while the GO term “ribosome genesis” is an associated biological process. On the basis of transcriptional freedom, our findings suggest that the regulation of gene expression can be modeled using only a few state variables. IMPORTANCE Yeast works like a well-organized factory. Each of its components works in its own way, while affecting the activities of others. The order of all activities is largely governed by the regulation of gene expression. In recent decades, biologists have recognized many regulations for yeast genes. However, it is not known how closely the regulation links each gene together to make all components of the cell work as a whole. In other words, biologists are very interested in how many independent control factors are needed to operate an artificial “cell” that works the same as a real one. In this work, we suggested that only 450 control factors were sufficient to represent the regulation of all 5800 yeast genes.
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影响因子：
7.7
作者：
Lim B
通讯作者：
Lim B
影响因子：
3.3
作者：
Mäkinen H;Sävilammi T;Papakostas S;Leder E;Vøllestad LA;Primmer CR
通讯作者：
Primmer CR
DOI：
10.1073/pnas.97.18.10101
发表时间：
2000-08-29
影响因子：
11.1
作者：
Alter, O;Brown, PO;Botstein, D
通讯作者：
Botstein, D
影响因子：
5.6
作者：
Lewis, Mitchell
通讯作者：
Lewis, Mitchell
DOI：
10.1073/pnas.0709146104
发表时间：
2007-11-20
影响因子：
11.1
作者：
Omberg, Larsson;Golub, Gene H.;Alter, Orly
通讯作者：
Alter, Orly