Journal
NUCLEIC ACIDS RESEARCH
Volume 37, Issue -, Pages D987-D991Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkn807
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Funding
- Center of Education and Research for Advanced Genome-based Medicine
- Ministry of Education, Culture, Sports, Science and Technology of Japan
- Institute of Medical Science, The University of Tokyo
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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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