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Bioinformatics. 2010 May 1;26(9):1267-8. doi: 10.1093/bioinformatics/btq121. Epub 2010 Mar 19.

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

Author information

1
Department of Biotechnology Research, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan.

Abstract

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/.

PMID:
20305269
DOI:
10.1093/bioinformatics/btq121
[Indexed for MEDLINE]

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