Identification of metagenes and their interactions through large-scale analysis of Arabidopsis gene expression data.
Identification of metagenes and their interactions through large-scale analysis of Arabidopsis gene expression data.
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DOI：
10.1186/1471-2164-13-237
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发表时间：
2012-06-13
期刊：
影响因子：
4.4
通讯作者：
Ge SX
中科院分区：
文献类型：
--
作者：
Wilson TJ;Lai L;Ban Y;Ge SX
许多植物基因已通过全基因组测序和深度转录组测序等方法得到鉴定；然而，我们对其中许多基因功能的了解仍然有限。大型基因表达数据集的整合和分析使研究人员能够形式化关于不同相关基因组之间功能和相互作用的假设。我们将非负矩阵分解（NMF）算法应用于AtGenExpress数据集，该数据集由783个微阵列样本（29个独立的实验系列）组成，以模式植物拟南芥为研究对象。我们鉴定了15个宏基因，它们是相关表达的基因群。通过基因集富集分析（GSEA）观察富集基因本体（GO）类别，确定了这些元基因的功能角色。还分析了这些元基因在不同实验条件下的活动水平，以将元基因与刺激/条件联系起来。在NMF分析的基础上，构建了一个元生关联网络，揭示了元生之间许多新的相互作用。将这些宏序列与早期的大规模聚类分析进行比较，可以发现许多统计上显著的重叠。本研究确定了一个由拟南芥基因组成的相关宏基因网络，这些基因在广泛的实验刺激中以高度相关的方式起作用，这可能会揭示许多未注释基因的功能。
Many plant genes have been identified through whole genome and deep transcriptome sequencing and other methods; yet our knowledge on the function of many of these genes remains limited. The integration and analysis of large gene-expression datasets gives researchers the ability to formalize hypotheses concerning the functionality and interaction between different groups of correlated genes. We applied the non-negative matrix factorization (NMF) algorithm to the AtGenExpress dataset which consists of 783 microarray samples (29 separate experimental series) conducted on the model plant Arabidopsis thaliana. We identified 15 metagenes, which are groups of genes with correlated expression. Functional roles of these metagenes are established by observing the enriched gene ontology (GO) categories using gene set enrichment analyses (GSEA). Activity levels of these metagenes in various experimental conditions are also analyzed to associate metagenes with stimuli/conditions. A metagene correlation network, constructed based on the results of NMF analysis, revealed many new interactions between the metagenes. Comparison of these metagenes with an earlier large-scale clustering analysis indicates many statistically significant overlaps. This study identifies a network of correlated metagenes composed of Arabidopsis genes acting in a highly correlated fashion across a broad spectrum of experimental stimuli, which may shed some light on the function of many of the un-annotated genes.
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影响因子：
7
作者：
Lee, HK;Hsu, AK;Pavlidis, P
通讯作者：
Pavlidis, P
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
1.9
作者：
Jiang, Xingpeng;Weitz, Joshua S.;Dushoff, Jonathan
通讯作者：
Dushoff, Jonathan
影响因子：
8
作者：
Inamura, K;Fujiwara, T;Ishikawa, Y
通讯作者：
Ishikawa, Y
影响因子：
--
作者：
Atias, Osnat;Chor, Benny;Chamovitz, Daniel A.
通讯作者：
Chamovitz, Daniel A.