COXPRESdb: a database of coexpressed gene networks in mammals

• DOI

Abstract

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.

BibTeX

@article{obayashi-nar200801,
    author = {Takeshi Obayashi and Shinpei Hayashi and Masayuki Shibaoka and Motoshi Saeki and Hiroyuki Ohta and Kengo Kinoshita},
    title = {{COXPRESdb}: a database of coexpressed gene networks in mammals},
    journal = {Nucleic Acids Research},
    volume = 36,
    number = {Database},
    pages = {D77--D82},
    doi = {10.1093/nar/gkm840},
    year = 2008,
}