Science China Life Sciences

, Volume 58, Issue 3, pp 276–286 | Cite as

AtGGM2014, an Arabidopsis gene co-expression network for functional studies

Open Access
Research Paper Special Topic: Plant Biology: Chromatin, Small RNA and Signaling

Abstract

Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the ArrayExpress database, we constructed an Arabidopsis gene co-expression network, termed AtGGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. AtGGM2014 offers a constructive tool for plant systems biology studies.

Keywords

Arabidopsis gene co-expression network graphical Gaussian model plant development stress response hormone response 

Supplementary material

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© The Author(s) 2015

This article is published under license to BioMed Central Ltd. Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.

Authors and Affiliations

  1. 1.Department of Plant Biology and the Genome Center, College of Biological SciencesUniversity of CaliforniaDavisUSA
  2. 2.Departments of Plant Biology and of Crop SciencesUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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