PromoterCAD: data-driven design of plant regulatory DNA

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 fro...

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Detalles Bibliográficos
Autores principales: Cox, Robert Sidney, Nishikata, Koro, Shimoyama, Sayoko, Yoshida, Yuko, Matsui, Minami, Makita, Yuko, Toyoda, Tetsuro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Articles
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692106/
https://www.ncbi.nlm.nih.gov/pubmed/23766287
http://dx.doi.org/10.1093/nar/gkt518
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author Cox, Robert Sidney
Nishikata, Koro
Shimoyama, Sayoko
Yoshida, Yuko
Matsui, Minami
Makita, Yuko
Toyoda, Tetsuro
author_facet Cox, Robert Sidney
Nishikata, Koro
Shimoyama, Sayoko
Yoshida, Yuko
Matsui, Minami
Makita, Yuko
Toyoda, Tetsuro
author_sort Cox, Robert Sidney
collection PubMed
description 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.
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spelling pubmed-36921062013-06-25 PromoterCAD: data-driven design of plant regulatory DNA Cox, Robert Sidney Nishikata, Koro Shimoyama, Sayoko Yoshida, Yuko Matsui, Minami Makita, Yuko Toyoda, Tetsuro Nucleic Acids Res Articles 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. Oxford University Press 2013-07 2013-06-12 /pmc/articles/PMC3692106/ /pubmed/23766287 http://dx.doi.org/10.1093/nar/gkt518 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Cox, Robert Sidney
Nishikata, Koro
Shimoyama, Sayoko
Yoshida, Yuko
Matsui, Minami
Makita, Yuko
Toyoda, Tetsuro
PromoterCAD: data-driven design of plant regulatory DNA
title PromoterCAD: data-driven design of plant regulatory DNA
title_full PromoterCAD: data-driven design of plant regulatory DNA
title_fullStr PromoterCAD: data-driven design of plant regulatory DNA
title_full_unstemmed PromoterCAD: data-driven design of plant regulatory DNA
title_short PromoterCAD: data-driven design of plant regulatory DNA
title_sort promotercad: data-driven design of plant regulatory dna
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692106/
https://www.ncbi.nlm.nih.gov/pubmed/23766287
http://dx.doi.org/10.1093/nar/gkt518
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