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Updated: Jul 6, 2026
08:09
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
Annotating genes of known and unknown function by large-scale coexpression analysis.
Kevin Horan1, Charles Jang, Julia Bailey-Serres
1Department of Botany and Plant Sciences , University of California, Riverside, CA 92521, USA.
Plant Physiology
|March 21, 2008
Summary
Researchers identified thousands of plant proteins of unknown function (PUFs) and linked them to biological processes and stress responses using gene expression data. This work aids in understanding plant biology and developing new crop traits.
Area of Science:
- Plant molecular biology
- Genomics
- Bioinformatics
Background:
- Approximately 40% of eukaryotic proteins, termed proteins of unknown function (PUFs), lack defined roles, posing a significant challenge in biological research.
- Functional characterization of PUFs is crucial for advancing our understanding of cellular mechanisms and biological processes.
Purpose of the Study:
- To identify PUF genes in Arabidopsis thaliana.
- To functionally annotate PUF genes by associating them with known biological processes and regulatory networks using large-scale gene expression data.
- To identify PUF genes involved in abiotic stress responses.
Main Methods:
- Identification of PUF genes through sequence similarity, domain-based, and empirical approaches.
- Genome-wide coexpression analysis of 1,310 Affymetrix expression chips to link PUF genes with proteins of known function (PKFs).
- Differential gene expression analysis to identify PUF and PKF genes responsive to various abiotic stresses.
Main Results:
- 1,541 PUF genes were associated with tightly coexpressed PKFs, with over 70% receiving refined biological process annotations.
- Highly overrepresented functional categories for PUFs included ribosome assembly, photosynthesis, and cell wall pathways.
- A significant number of PUF genes were identified as responsive to abiotic stresses, with some showing broad responses and others specific ones.
Conclusions:
- The study provides a comprehensive resource of coexpressed and differentially expressed PUF genes in Arabidopsis.
- The findings facilitate targeted functional characterization of PUFs and their roles in plant biology.
- A public database, the Plant Gene Expression Database, was developed to provide access to the generated gene expression data.
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