Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome.
Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome.
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DOI：
10.1038/s41526-023-00247-6
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发表时间：
2023-03-20
期刊：
影响因子：
5.1
通讯作者：
Gilroy, Simon
中科院分区：
文献类型：
--
作者：
Barker, Richard;Kruse, Colin P. S.;Johnson, Christina;Saravia-Butler, Amanda;Fogle, Homer;Chang, Hyun-Seok;Trane, Ralph Moller;Kinscherf, Noah;Villacampa, Alicia;Manzano, Aranzazu;Herranz, Raul;Davin, Laurence B.;Lewis, Norman G.;Perera, Imara;Wolverton, Chris;Gupta, Parul;Jaiswal, Pankaj;Reinsch, Sigrid S.;Wyatt, Sarah;Gilroy, Simon
太空飞行为植物提供了一个多方面的环境，结合了许多压力源和因素对植物生长的影响，包括重力变化，实验硬件的影响和辐射暴露的增加。为了帮助理解植物对这一系列复杂因素的反应，这项研究比较了美国国家航空航天局基因实验室数据库中存放的15个拟南芥太空飞行实验的转录组学分析。这些数据重新分析了在太空飞行与地面对照中显示显著差异表达的基因，使用单个通用计算管道用于微阵列或RNA-seq数据集。这种标准化的分析方法应大大提高数据集之间比较的可靠性。这种分析与广泛的交叉引用相结合，以策展与这些实验相关的元数据矩阵。我们的研究表明，分析类型（即，微阵列与RNA-seq）或环境和硬件条件对试图定义植物对太空飞行的反应的比较具有重要的混杂影响。元数据矩阵允许选择具有高相似性分数的研究，即，共享实验设计的多个元素，例如植物年龄或飞行硬件。这些研究之间的比较，然后有助于减少复杂性，得出结论所产生的比较实验之间的非常不同的设计。
Spaceflight presents a multifaceted environment for plants, combining the effects on growth of many stressors and factors including altered gravity, the influence of experiment hardware, and increased radiation exposure. To help understand the plant response to this complex suite of factors this study compared transcriptomic analysis of 15 Arabidopsis thaliana spaceflight experiments deposited in the National Aeronautics and Space Administration’s GeneLab data repository. These data were reanalyzed for genes showing significant differential expression in spaceflight versus ground controls using a single common computational pipeline for either the microarray or the RNA-seq datasets. Such a standardized approach to analysis should greatly increase the robustness of comparisons made between datasets. This analysis was coupled with extensive cross-referencing to a curated matrix of metadata associated with these experiments. Our study reveals that factors such as analysis type (i.e., microarray versus RNA-seq) or environmental and hardware conditions have important confounding effects on comparisons seeking to define plant reactions to spaceflight. The metadata matrix allows selection of studies with high similarity scores, i.e., that share multiple elements of experimental design, such as plant age or flight hardware. Comparisons between these studies then helps reduce the complexity in drawing conclusions arising from comparisons made between experiments with very different designs.
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影响因子：
48
作者：
Li T;Wernersson R;Hansen RB;Horn H;Mercer J;Slodkowicz G;Workman CT;Rigina O;Rapacki K;Stærfeldt HH;Brunak S;Jensen TS;Lage K
通讯作者：
Lage K
影响因子：
5.8
作者：
Fei, Teng;Yu, Tianwei
通讯作者：
Yu, Tianwei
影响因子：
3.6
作者：
Krishnamurthy A;Ferl RJ;Paul AL
通讯作者：
Paul AL
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
3
作者：
Bader, GD;Hogue, CW
通讯作者：
Hogue, CW