Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana
A comprehensive network of the Arabidopsis transcriptome was analyzed and may serve as a valuable resource for candidate gene function investigations. A web tool to explore module information was also provided.
Arabidopsis thaliana is a widely studied model plant whose transcriptome has been substantially profiled in various tissues, development stages and other conditions. These data can be reused for research on gene function through a systematic analysis of gene co-expression relationships. We collected microarray data from National Center for Biotechnology Information Gene Expression Omnibus, identified modules of co-expressed genes and annotated module functions. These modules were associated with experiments/traits, which provided potential signature modules for phenotypes. Novel heat shock proteins were implicated according to guilt by association. A higher-order module networks analysis suggested that the Arabidopsis network can be further organized into 15 meta-modules and that a chloroplast meta-module has a distinct gene expression pattern from the other 14 meta-modules. A comparison with the rice transcriptome revealed preserved modules and KEGG pathways. All the module gene information was available from an online tool at http://bioinformatics.fafu.edu.cn/arabi/. Our findings provide a new source for future gene discovery in Arabidopsis.
KeywordsRice Conservation Hub gene Transcriptome
Gene co-expression network
Weighted gene co-expression network analysis
National Centre for Biotechnology Information
Gene Expression Omnibus
Relative standard deviation
Kyoto Encyclopedia of Genes and Genomes
There are so many insightful literatures about gene co-expression analysis. The authors apologize that not all related studies were cited due to lack of space.
This work was supported in part by the National Natural Science Foundation of China (Grant numbers 31270454 and 81502091) and Open Project of Key laboratory of Loquat Germplasm Innovation and Utilization, Putian University, Fujian Province (Grant number 2017003).
Compliance with ethical standards
Conflicts of interest
The authors have no conflicts of interest to declare.
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