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Nucleic Acids Res. 2011 Jan;39(Database issue):D1016-22. doi: 10.1093/nar/gkq1147. Epub 2010 Nov 16.

COXPRESdb: a database to compare gene coexpression in seven model animals.

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1
Graduate School of Information Science, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan.

Abstract

Publicly available databases of coexpressed gene sets are a valuable resource for a wide variety of experimental studies, including gene targeting for functional identification, and for investigations of regulatory mechanisms or protein-protein interaction networks. Although coexpressed gene databases are becoming more and more popular in the field of plant biology, those with animal data are rather limited, possibly due to the lower reliability of the coexpression data. The original COXPRESdb (coexpressed gene database) (http://coxpresdb.jp) represented the coexpression relationship for human and mouse. Here, we report updates of this database that especially focus on the enhancement of the reliability of gene coexpression data in animals. For this purpose, we implemented a new comparable coexpression measure, Mutual Rank, included five other animal species, rat, chicken, zebrafish, fly and nematoda, to assess the conservation of coexpression, and added different layers of omics data into the integrated network of genes. Comparison of coexpression is a key concept to enhance the reliability of gene coexpression, and the integration of different information can reduce the noise inherent in the information. With the functions for gene network representation, COXPRESdb can help researchers to clarify the functional and regulatory networks of genes in a broad array of animal species.

PMID:
21081562
PMCID:
PMC3013720
DOI:
10.1093/nar/gkq1147
[Indexed for MEDLINE]
Free PMC Article
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