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COXPRESdb: a database to compare gene coexpression in seven model animals
Takeshi Obayashi1, Kengo Kinoshita
1Graduate School of Information Science, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.
Nucleic Acids Research
|November 18, 2010
Summary
This study enhances the COXPRESdb database for animal gene coexpression analysis. It improves data reliability using Mutual Rank and integrates diverse omics data for better gene network understanding.
Area of Science:
- Bioinformatics
- Genomics
- Systems Biology
Background:
- Coexpressed gene databases are crucial for biological research but animal data is limited.
- Existing animal coexpression data often suffers from lower reliability.
- The original COXPRESdb database focused on human and mouse coexpression.
Purpose of the Study:
- To enhance the reliability of gene coexpression data in animals.
- To expand the COXPRESdb database to include more animal species.
- To integrate multiple omics data layers for comprehensive gene network analysis.
Main Methods:
- Implemented Mutual Rank as a novel coexpression measure for improved reliability.
- Included five additional animal species: rat, chicken, zebrafish, fly, and nematoda.
- Integrated diverse omics data to create a layered gene network.
Main Results:
- Enhanced reliability of animal gene coexpression data through Mutual Rank.
- Expanded species coverage within COXPRESdb for broader comparative analysis.
- Developed an integrated gene network incorporating multiple omics layers.
Conclusions:
- The updated COXPRESdb provides a more reliable resource for animal gene coexpression studies.
- Comparative coexpression analysis aids in understanding gene regulatory networks.
- The database facilitates functional and regulatory network elucidation across various animal species.
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