TY - JOUR
T1 - ATTED-II provides coexpressed gene networks for Arabidopsis
AU - Obayashi, Takeshi
AU - Hayashi, Shinpei
AU - Saeki, Motoshi
AU - Ohta, Hiroyuki
AU - Kinoshita, Kengo
N1 - Funding Information:
This work was partially supported by a Grant-in Aid for Scientific Research on the Priority Area ‘Transportsome’ and by the Global COE Program (Center of Education and Research for Advanced Genome-based Medicine) from the Ministry of Education, Culture, Sports, Science and Technology of Japan. Funding for open access charges: Annual budget for Human Genome Center, Institute of Medical Science, The University of Tokyo.
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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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U2 - 10.1093/nar/gkn807
DO - 10.1093/nar/gkn807
M3 - Article
C2 - 18953027
AN - SCOPUS:58149197587
SN - 0305-1048
VL - 37
SP - D987-D991
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - SUPPL. 1
ER -