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 <i>cis</i>-regulatory elements. Recently, we have expanded PromoterCAD’s scope with additional plant and animal data: (1) PLACE (Plant <i>Cis</i>-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 <i>Arabidopsis thaliana</i> 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 <i>Mus musculus</i> 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