Journal Article

CoP: a database for characterizing co-expressed gene modules with biological information in plants

Yoshiyuki Ogata, Hideyuki Suzuki, Nozomu Sakurai and Daisuke Shibata

in Bioinformatics

Volume 26, issue 9, pages 1267-1268
Published in print May 2010 | ISSN: 1367-4803
Published online March 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq121
CoP: a database for characterizing co-expressed gene modules with biological information in plants

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Summary: Using a large dataset (10 022 assays) obtained from public plant microarray databases, we developed the CoP database for associating co-expressed gene modules with biological information such as gene ontology terms and, if available, metabolic pathway names. The Confeito algorithm developed previously in our laboratory, which is suitable to calculate the interconnectivity between genes in co-expressed gene network, was applied to extract co-expressed gene modules. The database includes the gene modules for Arabidopsis thaliana (thale cress) and seven crops, Glycine max (soybean), Hordeum vulgare (barley), Oryza sativa (rice), Populus trichocarpa (poplar), Triticum aestivum (wheat), Vitis vinifera (grape) and Zea mays (maize).

Availability: The CoP database is available at: http://webs2.kazusa.or.jp/kagiana/cop0911/

Contact: shibata@kazusa.or.jp

Journal Article.  1355 words. 

Subjects: Bioinformatics and Computational Biology

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