ATTED-II provides coexpressed gene networks for Arabidopsis

Takeshi Obayashi, Shinpei Hayashi, Motoshi Saeki, Hiroyuki Ohta, Kengo Kinoshita

Research output: Contribution to journalArticlepeer-review

289 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)D987-D991
JournalNucleic acids research
Volume37
Issue numberSUPPL. 1
DOIs
Publication statusPublished - 2009
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'ATTED-II provides coexpressed gene networks for Arabidopsis'. Together they form a unique fingerprint.

Cite this