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

Abstract

Summary: Using a large dataset (10022 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. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org.