ATTED-II provides coexpressed gene networks for Arabidopsis

• DOI

Abstract

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.

BibTeX

@article{obayashi-nar200901,
    author = {Takeshi Obayashi and Shinpei Hayashi and Motoshi Saeki and Hiroyuki Ohta and Kengo Kinoshita},
    title = {{ATTED-II} provides coexpressed gene networks for Arabidopsis},
    journal = {Nucleic Acids Research},
    volume = 37,
    number = {Database},
    pages = {D987--D991},
    doi = {10.1093/nar/gkn807},
    year = 2009,
}