| URL: | http://promotercad.org |
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| Description: | Synthetic promoters can be used to control when, where, and how much of an arbitrary gene is expressed in an organism. The regulation of a promoter is specified by its pattern of cis-regulatory motifs; several methods have been developed for identifying and predicting the functions of natural motifs. Synthetic promoters with novel regulation functions can be designed by rational motif arrangement. PromoterCAD is a simple web-based UI for data-driven regulatory DNA design. Plugin tools are used to mine regulatory motifs from public databases, with an iterative design workflow for the accumulation of many motifs within a synthetic promoter design. The UI arbitrates when different introduced motifs overlap in position. Currently, PromoterCAD uses data collected from Arabidopsis thaliana to aid synthetic plant promoter design. |
| Year founded: | 2014 |
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Accessible
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| Country/Region: | Japan |
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| University/Institution: | RIKEN |
| Address: | Integrated Database Unit, Advanced Center for Computing and Communication (ACCC), RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. |
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| Country/Region: | Japan |
| Contact name (PI/Team): | Minami Matsui |
| Contact email (PI/Helpdesk): | minami@riken.jp |
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Database construction for PromoterCAD: synthetic promoter design for mammals and plants. [PMID: 24364365]
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. |