Journal Article

ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants

Takeshi Obayashi, Kozo Nishida, Kota Kasahara and Kengo Kinoshita

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 52, issue 2, pages 213-219
Published in print February 2011 | ISSN: 0032-0781
Published online January 2011 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcq203

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ATTED-II (http://atted.jp) is a gene coexpression database for a wide variety of experimental designs, such as prioritizations of genes for functional identification and analyses of the regulatory relationships among genes. Here, we report updates of ATTED-II focusing on two new features: condition-specific coexpression and homologous coexpression with rice. To analyze a broad range of biological phenomena, it is important to collect data under many diverse experimental conditions, but the meaning of coexpression can become ambiguous under these conditions. One approach to overcome this difficulty is to calculate the coexpression for each set of conditions with a clear biological meaning. With this viewpoint, we prepared five sets of experimental conditions (tissue, abiotic stress, biotic stress, hormones and light conditions), and users can evaluate the coexpression by employing comparative gene lists and switchable gene networks. We also developed an interactive visualization system, using the Cytoscape web system, to improve the network representation. As the second update, rice coexpression is now available. The previous version of ATTED-II was specifically developed for Arabidopsis, and thus coexpression analyses for other useful plants have been difficult. To solve this problem, we extended ATTED-II by including comparison tables between Arabidopsis and rice. This representation will make it possible to analyze the conservation of coexpression among flowering plants. With the ability to investigate condition-specific coexpression and species conservation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in a broad array of plant species.

Keywords: Arabidopsis; Comparative transcriptomics; Database; Gene coexpression; Gene network; Rice

Journal Article.  3636 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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