Coexpression characteristics of trehalose-6-phosphate phosphatase subfamily genes reveal different functions in a network context
Coexpression characteristics of trehalose-6-phosphate phosphatase subfamily genes reveal different functions in a network context
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DOI：
10.1111/j.1399-3054.2008.01101.x
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发表时间：
2008-07-01
影响因子：
6.4
通讯作者：
Bohnert, Hans J.
中科院分区：
文献类型：
--
作者：
Li, Pinghua;Ma, Shisong;Bohnert, Hans J.
拟南芥数据库突出了转录组在数百次实验操作下的行为，使得将这些信息整合到基因网络中的尝试成为可能。我们展示并讨论了使用沉积微阵列实验生成的基因网络模型的功能。该网络基于图形高斯模型，描述了在各种外部因素以及非生物、生物和化学处理下基因的条件共调节。在这项研究中，我们展示了该网络的一个方面，该网络与家族中的基因功能有关，其中所有成员似乎都进行相同的生化反应。本研究选择了拟南芥基因组中编码海藻糖-6-磷酸磷酸酶 (TPP) 的 10 个基因。网络突出显示了其中九个基因。一般来说，每个 TPP 形成一个与识别不同功能类别的基因相关的网络。因此，获得了网络结构，确定了与碳分布、干旱、寒冷、病原体反应、钙和活性氧/氧化还原特征的联系，包括将不同TPP基因播种的网络图分开的转录控制基因。转录共表达网络的结构通过将基因家族的不同成员关联到单独的簇中，促进了假设的建立和对家族中单个基因功能的深入研究。
Arabidopsis thaliana databases are available that highlight the behavior of the transcriptome under literally hundreds of experimental manipulations, making attempts possible that integrate this information into gene networks. We present and discuss the functioning of a gene network model generated using deposited microarray experiments. Based on a graphical Gaussian model, the network describes conditional coregulation of genes under a variety of external factors and abiotic, biotic and chemical treatments. In this study, we show an aspect of this network that pertains to functions of genes in families where all members appear to carry out the same biochemical reaction. Chosen in this study were 10 genes in the Arabidopsis genome encoding trehalose-6-phosphate phosphatases (TPPs). Nine of these genes were highlighted by the network. Generally, each TPP formed a network associated with genes that identify different functional categories. Thus, network structures were obtained that identified connections to carbon distribution, drought, cold, pathogen responses, calcium and reactive oxygen species/redox signatures, including transcriptional control genes that separated network graphs seeded with different TPP genes. The structure of the transcript coexpression networks, by associating diverse members of gene families into separate clusters, facilitates hypothesis building and in-depth studies of functions of individual genes in families.