- © 2013 American Society of Plant Biologists. All rights reserved.
Abstract
Gene expression profiling studies are usually performed on pooled samples grown under tightly controlled experimental conditions to suppress variability among individuals and increase experimental reproducibility. In addition, to mask unwanted residual effects, the samples are often subjected to relatively harsh treatments that are unrealistic in a natural context. Here, we show that expression variations among individual wild-type Arabidopsis thaliana plants grown under the same macroscopic growth conditions contain as much information on the underlying gene network structure as expression profiles of pooled plant samples under controlled experimental perturbations. We advocate the use of subtle uncontrolled variations in gene expression between individuals to uncover functional links between genes and unravel regulatory influences. As a case study, we use this approach to identify ILL6 as a new regulatory component of the jasmonate response pathway.
Glossary
- ANOVA
- analysis of variance
- GO
- Gene Ontology
- FDR
- false discovery rate
- JA
- jasmonic acid
- ABA
- abscisic acid
- JA-Ile
- jasmonoyl-Ile
- Col-0
- Columbia-0
- MeJA
- methyl jasmonate
- Received April 3, 2013.
- Revised June 16, 2013.
- Accepted July 18, 2013.
- Published August 13, 2013.