Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice
Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice
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DOI：
10.1104/pp.111.173047
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发表时间：
2011-07-01
期刊：
影响因子：
7.4
通讯作者：
Feltus, F. Alex
中科院分区：
文献类型：
--
作者：
Ficklin, Stephen P.;Feltus, F. Alex
植物生物学的一个主要目标是发现复杂性状背后的分子子系统。在系统遗传学方法中结合使用遗传和基因组资源为实现这一目标提供了一种手段。本研究描述了一个玉米（Zea mays）基因共表达网络建立在公开可用的表达阵列。该网络由2071个基因座组成，分为34个不同的模块，包含1928个丰富的功能注释项和35个协同功能基因簇。值得注意的是，发现391个功能未知的玉米基因与功能已知的基因在模块内共表达。在这个玉米网络和先前描述的水稻（Oryza sativa）共表达网络之间进行了全球网络比对。使用IsoRankN工具，该工具结合了基因同源性和网络拓扑结构进行比对。在两个草网络中共检测到1173个对齐的位点，这些位点被浓缩成154个保守子图，其中水稻中保存了4758个共表达边，玉米中保存了6105个共表达边。该研究提供了对玉米共表达空间的早期看法，并为这两个重要农业物种之间的功能基因组和遗传信息的翻译提供了一个初步的基于网络的框架。
One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.