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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

PLANEX: the plant co-expression database.

Won Cheol Yim¹, Yongbin Yu, Kitae Song

¹Department of Plant Biotechnology, Dongguk Univ-Seoul, Seoul 100-715, Korea.

BMC Plant Biology

|May 22, 2013

Summary

The PLAnt co-EXpression database (PLANEX) offers a new resource for plant gene co-expression analysis across eight species. It aids in functional gene identification and comparative genomics for researchers studying plant gene relationships.

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Area of Science:

Plant genomics
Bioinformatics
Computational biology

Background:

Limited gene co-expression information exists for plants.
The PLAnt co-EXpression database (PLANEX) addresses this gap.
PLANEX utilizes publicly available GeneChip data from the National Center for Biotechnology Information (NCBI).

Purpose of the Study:

To develop a genome-wide co-expression database for plant gene analysis.
To facilitate functional gene identification and analysis of gene dependency.
To provide a comprehensive resource for plant gene co-expression data.

Main Methods:

Constructed a co-expression database for eight plant species: Arabidopsis thaliana, Glycine max, Hordeum vulgare, Oryza sativa, Solanum lycopersicum, Triticum aestivum, Vitis vinifera, and Zea mays.
Calculated Pearson's correlation coefficients (PCCs) for co-expressed genes.
Performed Gene Ontology (GO) enrichment tests and Cohen's Kappa analysis for functional similarity.
Generated co-expression cluster networks using the k-mean method.

Main Results:

PLANEX provides a correlation database, cluster networks, and enrichment test interpretations for eight plant species.
The database facilitates the identification of hundreds of co-expressed genes for enrichment analysis.
A 'Co-expression gene compare' feature enables comparative genomics analysis of co-expressed genes.

Conclusions:

PLANEX serves as a valuable resource for plant gene co-expression analysis and functional genomics.
The database aids in interpreting experimental data and identifying commonalities among genes of interest.
It supports comparative genomics approaches for understanding plant gene relationships.