Microarray meta-analysis to explore abiotic stress-specific gene expression patterns in Arabidopsis

Botanical Studies
Po-Chih ShenLi-Yu Daisy Liu

Abstract

Abiotic stresses are the major limiting factors that affect plant growth, development, yield and final quality. Deciphering the underlying mechanisms of plants' adaptations to stresses using few datasets might overlook the different aspects of stress tolerance in plants, which might be simultaneously and consequently operated in the system. Fortunately, the accumulated microarray expression data offer an opportunity to infer abiotic stress-specific gene expression patterns through meta-analysis. In this study, we propose to combine microarray gene expression data under control, cold, drought, heat, and salt conditions and determined modules (gene sets) of genes highly associated with each other according to the observed expression data. By analyzing the expression variations of the Eigen genes from different conditions, we had identified two, three, and five gene modules as cold-, heat-, and salt-specific modules, respectively. Most of the cold- or heat-specific modules were differentially expressed to a particular degree in shoot samples, while most of the salt-specific modules were differentially expressed to a particular degree in root samples. A gene ontology (GO) analysis on the stress-specific modules suggested that the g...Continue Reading

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Citations

Dec 11, 2019·International Journal of Molecular Sciences·Zhongyu LiuJianbing Qin
Jan 20, 2019·International Journal of Molecular Sciences·Anna PiaseckaMaciej Stobiecki
Aug 16, 2019·International Journal of Molecular Sciences·Komivi DossaXiurong Zhang
Feb 13, 2021·NAR Genomics and Bioinformatics·Christina B AzodiShin-Han Shiu
Jan 2, 2022·Plant Molecular Biology·Napaporn Sriden, Varodom Charoensawan

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Methods Mentioned

BETA
RNA-Seq

Software Mentioned

RMAExpress
WGCNA package
agriGO
R
WGCNA

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