Database Construction for Synthetic Promoter Design Web Application (PromoterCAD)

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Koro Nishikata, Robert Sidney COX III, Sayoko SHIMOYAMA, Yuko YOSHIDA, Minami MATSUI, Tetsuro TOYODA

Bioinformatics And Systems Engineering division (BASE), Japan

We use gene transformation techniques to produce useful materials for bioengineering. In using plants to produce useful materials, plant growth inhibition might reduce product yield, as a consequence of gene transformation. This transgenic growth inhibition might be avoided by limiting gene expression to a specific tissue type or phase of plant growth. For this reason we use appropriate control of gene expression to overcome product yield reduction. In this study we constructed web application and databases to design the synthetic promoter to control gene expression of any organism in a tissue or time specific manner (PromoterCAD). We collected genomic and transcriptomic data using the Semantic Web system LinkData/LinkDataApp, and developed applications to design synthetic promoters by novel arrangement of cis-regulatory elements. We made 4 types of expression-motif sequence data by combining 2 types of expression data (AtGenExpress, Diurnal) and 2 types of regulatory sequence motif (ATTED-II, PPDB). These include information on 21,000 genes from Arabidopsis and 1,410,000 microarray data measurements in 20 growth conditions and 79 tissue organs and developmental stages. The application provides a graphical user interface (GUI), so users can design promoters easily. Users select tissue and developmental stages and circadian expression conditions. Next, the application will provide appropriate motif sequences if users select tools picking maximum and minimum for expression data as well as phase and amplitude of circadian rhythms. Users will then achieve a designed sequence by replacing the original sequence with the motif sequences. Thus we could design the synthetic promoters, which increase production yields. Furthermore, Users can expand the scope of PromoterCAD with additional data including other plant and animal resources (e.g. tomato, mouse). We will present adding PLACE (Plant Cis-acting Regulatory DNA Elements) database, including multiple sizes of sequence motifs in SB6.0. PromoterCAD URL: http://promotercad.org LinkData URL: http://linkdata.org