TY - JOUR
T1 - COXPRESdb
T2 - A database of coexpressed gene networks in mammals
AU - Obayashi, Takeshi
AU - Hayashi, Shinpei
AU - Shibaoka, Masayuki
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’ from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan to KK. Computation time was provided by the Super Computer System, Human Genome Center, Institute of Medical Science, The University of Tokyo. Funding to pay the Open Access publication charges for this article was provided by MEXT of Japan.
PY - 2008/1
Y1 - 2008/1
N2 - A database of coexpressed gene sets can provide valuable information for a wide variety of experimental designs, such as targeting of genes for functional identification, gene regulation and/or protein - protein interactions. Coexpressed gene databases derived from publicly available GeneChip data are widely used in Arabidopsis research, but platforms that examine coexpression for higher mammals are rather limited. Therefore, we have constructed a new database, COXPRESdb (coexpressed gene database) (http://coxpresdb.hgc.jp) for coexpressed gene lists and networks in human and mouse. Coexpression data could be calculated for 19 777 and 21 036 genes in human and mouse, respectively, by using the GeneChip data in NCBI GEO. COXPRESdb enables analysis of the four types of coexpression networks: (i) highly coexpressed genes for every gene, (ii) genes with the same GO annotation, (iii) genes expressed in the same tissue and (iv) user-defined gene sets. When the networks became too big for the static picture on the web in GO networks or in tissue networks, we used Google Maps API to visualize them interactively. COXPRESdb also provides a view to compare the human and mouse coexpression patterns to estimate the conservation between the two species.
AB - A database of coexpressed gene sets can provide valuable information for a wide variety of experimental designs, such as targeting of genes for functional identification, gene regulation and/or protein - protein interactions. Coexpressed gene databases derived from publicly available GeneChip data are widely used in Arabidopsis research, but platforms that examine coexpression for higher mammals are rather limited. Therefore, we have constructed a new database, COXPRESdb (coexpressed gene database) (http://coxpresdb.hgc.jp) for coexpressed gene lists and networks in human and mouse. Coexpression data could be calculated for 19 777 and 21 036 genes in human and mouse, respectively, by using the GeneChip data in NCBI GEO. COXPRESdb enables analysis of the four types of coexpression networks: (i) highly coexpressed genes for every gene, (ii) genes with the same GO annotation, (iii) genes expressed in the same tissue and (iv) user-defined gene sets. When the networks became too big for the static picture on the web in GO networks or in tissue networks, we used Google Maps API to visualize them interactively. COXPRESdb also provides a view to compare the human and mouse coexpression patterns to estimate the conservation between the two species.
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U2 - 10.1093/nar/gkm840
DO - 10.1093/nar/gkm840
M3 - Article
C2 - 17932064
AN - SCOPUS:38549180536
SN - 0305-1048
VL - 36
SP - D77-D82
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - SUPPL. 1
ER -