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Nucleic Acids Research Advance Access published online on October 25, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn807
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

ATTED-II provides coexpressed gene networks for Arabidopsis

Takeshi Obayashi1,*, Shinpei Hayashi2, Motoshi Saeki2, Hiroyuki Ohta3 and Kengo Kinoshita1,4

1Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, 2Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, 3Center of Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B65, Nagatsuta-cho, Midori-ku, Yokohama 266-8501 and 4Bioinformatics Research and Development, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan

*To whom correspondence should be addressed. Tel: +81 3 5449 5131; Fax: +81 3 5449 5133; Email: takeshi.obayashi{at}atted.jp

Received September 14, 2008. Revised October 9, 2008. Accepted October 10, 2008.

ATTED-II (http://atted.jp) is a database of gene coexpression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory relationships. Here, we report updates of ATTED-II that focus especially on functionalities for constructing gene networks with regard to the following points: (i) introducing a new measure of gene coexpression to retrieve functionally related genes more accurately, (ii) implementing clickable maps for all gene networks for step-by-step navigation, (iii) applying Google Maps API to create a single map for a large network, (iv) including information about protein–protein interactions, (v) identifying conserved patterns of coexpression and (vi) showing and connecting KEGG pathway information to identify functional modules. With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis.


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