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Planta

, Volume 249, Issue 5, pp 1487–1501 | Cite as

Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana

  • Wei LiuEmail author
  • Liping Lin
  • Zhiyuan Zhang
  • Siqi Liu
  • Kuan Gao
  • Yanbin Lv
  • Huan Tao
  • Huaqin HeEmail author
Original Article

Abstract

Main conclusion

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.

Keywords

Rice Conservation Hub gene Transcriptome 

Abbreviations

GCN

Gene co-expression network

WGCNA

Weighted gene co-expression network analysis

NCBI

National Centre for Biotechnology Information

GEO

Gene Expression Omnibus

RSD

Relative standard deviation

GO

Gene ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

Notes

Acknowledgements

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.

Funding

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.

Supplementary material

425_2019_3102_MOESM1_ESM.xlsx (595 kb)
Supplementary material 1 (xlsx 595 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.School of Life SciencesFujian Agriculture and Forestry UniversityFuzhouPeople’s Republic of China

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