title: Database construction for PromoterCAD: synthetic promoter design for mammals and plants.
abstract: Synthetic promoters can control a gene's timing, location, and expression level. The PromoterCAD web server ( http://promotercad.org ) allows the design of synthetic promoters to control plant gene expression, by novel arrangement of cis-regulatory elements. Recently, we have expanded PromoterCAD's scope with additional plant and animal data: (1) PLACE (Plant Cis-acting Regulatory DNA Elements), including various sized sequence motifs; (2) PEDB (Mammalian Promoter/Enhancer Database), including gene expression data for mammalian tissues. The plant PromoterCAD data now contains 22 000 Arabidopsis thaliana genes, 2 200 000 microarray measurements in 20 growth conditions and 79 tissue organs and developmental stages, while the new mammalian PromoterCAD data contains 679 Mus musculus genes and 65 000 microarray measurements in 96 tissue organs and cell types ( http://promotercad.org/mammal/ ). This work presents step-by-step instructions for adding both regulatory motif and gene expression data to PromoterCAD, to illustrate how users can expand PromoterCAD functionality for their own applications and organisms.
authors.affiliation: Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Koro
authors.initials: K
authors.lastname: Nishikata
authors.forename: Robert Sidney
authors.initials: RS
authors.lastname: Cox
authors.forename: Sayoko
authors.initials: S
authors.lastname: Shimoyama
authors.forename: Yuko
authors.initials: Y
authors.lastname: Yoshida
authors.forename: Minami
authors.initials: M
authors.lastname: Matsui
authors.forename: Yuko
authors.initials: Y
authors.lastname: Makita
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
mesh_terms: D000818:Animals; D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020407:Internet; D008322:Mammals / Q000235:genetics; D010944:Plants / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012984:Software; D058615:Synthetic Biology / Q000379:methods*