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Updated: Mar 30, 2026
08:09
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
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ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.
Yuichi Aoki1, Yasunobu Okamura2, Shu Tadaka2
1Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
Plant & Cell Physiology
|November 8, 2015
Summary
The updated ATTED-II database (version 8.0) enhances plant gene coexpression analysis by integrating new microarray and RNA sequencing data for diverse species. This improves the reliability of identifying conserved gene functions and lineage-specific expression patterns.
Area of Science:
- Plant biology
- Bioinformatics
- Genomics
Background:
- Gene coexpression analysis is crucial for understanding gene function and relationships.
- Existing coexpression databases often suffer from low reliability in standalone analyses.
- Evolutionarily conserved coexpression offers higher reliability and evolutionary significance.
Purpose of the Study:
- To report updates to the ATTED-II coexpression database (version 8.0).
- To enhance plant gene functional studies through improved coexpression data and analysis tools.
- To provide reliable lineage-specific coexpression information for dicot and monocot species.
Main Methods:
- Integration of new microarray and RNA sequencing coexpression data for seven dicot and two monocot species.
- Inclusion of updated network analysis tools within the ATTED-II platform.
- Assessment of coexpression data set quality and reliability.
Main Results:
- ATTED-II version 8.0 now includes eight microarray- and six RNA sequencing-based datasets.
- The quality of new coexpression datasets is higher than previous ones.
- Five species are now supported by both microarray and RNA sequencing data, increasing reliability.
- Lineage-specific coexpression, such as for cell wall genes in monocots and dicots, can now be explored.
Conclusions:
- ATTED-II version 8.0 offers expanded, high-quality coexpression data for plant research.
- The database facilitates reliable identification of functional gene relationships and evolutionary conserved patterns.
- ATTED-II provides new avenues for investigating lineage-specific evolution in plants.
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