title: PromoterCAD: Data-driven design of plant regulatory DNA.
abstract: Synthetic promoters can control the timing, location and amount of gene expression for any organism. PromoterCAD is a web application for designing synthetic promoters with altered transcriptional regulation. We use a data-first approach, using published high-throughput expression and motif data from for Arabidopsis thaliana to guide DNA design. We demonstrate data mining tools for finding motifs related to circadian oscillations and tissue-specific expression patterns. PromoterCAD is built on the LinkData open platform for data publication and rapid web application development, allowing new data to be easily added, and the source code modified to add new functionality. PromoterCAD URL: http://promotercad.org. LinkData URL: http://linkdata.org.
authors.affiliation: Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Robert Sidney
authors.initials: RS
authors.lastname: Cox
authors.forename: Koro
authors.initials: K
authors.lastname: Nishikata
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: D017360:Arabidopsis / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry*; D057225:Data Mining; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D020407:Internet; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D012984:Software; D014158:Transcription, Genetic
chemical_list: D018744:DNA, Plant