Nishikata Koro, Cox Robert Sidney, Shimoyama Sayoko, Yoshida Yuko, Matsui Minami, Makita Yuko, Toyoda Tetsuro
Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
ACS Synth Biol. 2014 Mar 21;3(3):192-6. doi: 10.1021/sb400178c. Epub 2014 Jan 6.
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.
