Evolutionary-conserved gene expression response profiles across mammalian tissues
Evolutionary-conserved gene expression response profiles across mammalian tissues
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DOI：
10.1089/omi.2006.0007
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发表时间：
2007-03-01
影响因子：
3.3
通讯作者：
States, David J.
中科院分区：
文献类型：
--
作者：
Chen, Ji;Blackwell, Thomas W.;States, David J.
基因表达反应是复杂的，并且经常涉及许多基因的作用以实现协调模式。我们假设这些协调反应在进化上是保守的，并使用人类和小鼠基因表达谱的比较来识别一组正常哺乳动物组织中最显着的保守特征。根据人类和小鼠多个组织的多项研究数据，使用主成分分析在每个物种中鉴定出了跨多个组织的 13 种基因表达模式。引人注目的是，在从两个物种独立获得的 13 个模式中，有 12 个模式观察到了人类和小鼠模式的 1 对 1 配对。这些配对模式定义了进化保守的基因表达响应模式（CGEM）。值得注意的是，在这项研究中，我们能够提取出不会被实验室间或物种间变异所淹没的生物反应。在我们的基因表达数据集中，84% 的变异可以使用这些 CGEM 来解释。使用基因本体、通路和转录因子结合位点表达进行功能注释。我们的结论是，我们找到了一种获得保守基因反应模式的无偏见方法，该模式解释了给定数据集中相当一部分基因表达变异，并验证了哺乳动物中主要基因表达反应模式的保守性。
Gene expression responses are complex and frequently involve the actions of many genes to effect coordinated patterns. We hypothesized these coordinated responses are evolutionarily conserved and used a comparison of human and mouse gene expression profiles to identify the most prominent conserved features across a set of normal mammalian tissues. Based on data from multiple studies across multiple tissues in human and mouse, 13 gene expression modes across multiple tissues were identified in each of these species using principal component analysis. Strikingly, 1-to-1 pairing of human and mouse modes was observed in 12 out of 13 modes obtained from the two species independently. These paired modes define evolutionarily conserved gene expression response modes (CGEMs). Notably, in this study we were able to extract biological responses that are not overwhelmed by laboratory-to-laboratory or species-to-species variation. Of the variation in our gene expression dataset, 84% can be explained using these CGEMs. Functional annotation was performed using Gene Ontology, pathway, and transcription factor binding site over representation. Our conclusion is that we found an unbiased way of obtaining conserved gene response modes that accounts for a considerable portion of gene expression variation in a given dataset, as well as validates the conservation of major gene expression response modes across the mammals.