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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

Gene coexpression analysis in Arabidopsis thaliana based on public microarray data.

Vasileios L Zogopoulos¹, Apostolos Malatras², Ioannis Michalopoulos¹

¹Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.

|March 4, 2022

Summary

This study presents a method for creating gene coexpression trees in Arabidopsis thaliana using microarray data. It includes an automated quality control step for reliable functional gene discovery.

Keywords:

Bioinformatics Genomics Model Organisms Plant sciences Systems biology

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Area of Science:

Genomics
Bioinformatics
Plant Biology

Background:

Gene coexpression analysis is crucial for understanding gene function and biological pathways.
Identifying functional gene partners or assigning roles to unknown genes relies on coexpression patterns.

Purpose of the Study:

To describe a protocol for constructing a gene coexpression tree for Arabidopsis thaliana.
To detail an automated quality control approach for microarray data analysis.

Main Methods:

Utilizing publicly available Affymetrix CEL microarray data from Arabidopsis thaliana.
Implementing an automated quality control procedure to ensure sample integrity.
Constructing a gene coexpression tree based on the analyzed data.

Main Results:

The protocol enables the creation of a gene coexpression tree for Arabidopsis thaliana.
The automated quality control enhances the reliability of computational gene coexpression analysis.
This method facilitates the discovery of functional gene relationships.

Conclusions:

Gene coexpression trees provide insights into related biological processes.
The presented protocol and quality control method support functional genomics research in plants.
This approach aids in assigning biological roles to genes of unknown function.