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Published March 29, 2016 | Version v1
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Data from: Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants

Description

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.

Notes

Supplemental Dataset 1
Module figures for all modules learned from the residuals dataset.
Supplemental Dataset 2
Excel file containing predicted GO annotations for all modules in Supplemental Data Set 1.
tpc112268SupplementalDS2.xlsx
Supplemental Dataset 3
Module figures for all modules learned from the original dataset, without removing lab and accession effects.
Supplemental Dataset 4
Excel file containing predicted GO annotations for all modules in Supplemental Data Set 3.
tpc112268SupplementalDS4.xlsx
Supplemental Dataset 5
Excel file with gene counts in the residuals and sample networks for all GO processes with at least 10 nodes in the residuals network.
tpc112268SupplementalDS5.xlsx
Supplemental Dataset 6
Category-specific function prediction performance figures for all GO categories scored in Supplemental Figure 5.
tpc112268SupplementalDS6.pdf

Files

Supplemental Dataset 1.pdf

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Additional details

Related works

Is cited by
10.1105/tpc.113.112268 (DOI)