Gene network landscape of the ciliate Tetrahymena thermophila.
Gene network landscape of the ciliate Tetrahymena thermophila.
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DOI：
10.1371/journal.pone.0020124
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Miao W
中科院分区：
文献类型：
--
作者：
Xiong J;Yuan D;Fillingham JS;Garg J;Lu X;Chang Y;Liu Y;Fu C;Pearlman RE;Miao W
基因微阵列的全基因组表达数据可用于推断基因网络。在细胞水平上，基因网络呈现出基因紧密连接的模块以及与其他基因高度连接的枢纽基因的情况。基因网络有助于识别参与同一通路、蛋白质复合物中或共同受调控的基因。在这项研究中，我们使用不同的方法在纤毛虫嗜热四膜虫中寻找基因网络，并描述了该网络的一些重要特性，比如模块和枢纽。
利用67个单通道微阵列，我们使用三种方法构建了嗜热四膜虫基因网络（TGN）：皮尔逊相关系数（PCC）、斯皮尔曼相关系数（SCC）以及关联背景可能性（CLR）算法。使用酵母中的四种保守蛋白质复合物对这三个网络的准确性和覆盖度进行了评估。确定Z分数阈值为3.49的CLR网络是最稳健的。对TGN进行了划分，发现了55个模块。此外，对任意确定的1200个枢纽的分析表明，根据它们的表达谱，这些枢纽可分为六组。我们还研究了在酵母中缺失的嗜热四膜虫中的人类疾病同源基因，并提供证据表明其中一些在嗜热四膜虫中参与的过程与在人类中相同。
这项研究构建了一个嗜热四膜虫基因网络，为该生物网络的特性提供了新的见解，并为在通路水平上研究嗜热四膜虫基因提供了重要资源。
Genome-wide expression data of gene microarrays can be used to infer gene networks. At a cellular level, a gene network provides a picture of the modules in which genes are densely connected, and of the hub genes, which are highly connected with other genes. A gene network is useful to identify the genes involved in the same pathway, in a protein complex or that are co-regulated. In this study, we used different methods to find gene networks in the ciliate Tetrahymena thermophila, and describe some important properties of this network, such as modules and hubs. Using 67 single channel microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient (PCC), the Spearman correlation coefficient (SCC) and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast. The CLR network with a Z-score threshold 3.49 was determined to be the most robust. The TGN was partitioned, and 55 modules were found. In addition, analysis of the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to their expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and provide evidence indicating that some of these are involved in the same process in Tetrahymena as in human. This study constructed a Tetrahymena gene network, provided new insights to the properties of this biological network, and presents an important resource to study Tetrahymena genes at the pathway level.
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影响因子：
9.8
作者：
Bénit, P;Chretien, D;Rötig, A
通讯作者：
Rötig, A
影响因子：
64.5
作者：
Brownell, JE;Zhou, JX;Allis, CD
通讯作者：
Allis, CD
影响因子：
3
作者：
Cerulo L;Elkan C;Ceccarelli M
通讯作者：
Ceccarelli M
DOI：
10.1073/pnas.122653799
发表时间：
2002-06-11
影响因子：
11.1
作者：
Girvan, M;Newman, MEJ
通讯作者：
Newman, MEJ
影响因子：
5.3
作者：
Bednenko, Janna;Noto, Tomoko;Gorovsky, Martin A.
通讯作者：
Gorovsky, Martin A.