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Below is a description of the PromoterCAD Application. 


Title: Synthetic Plant Promoter Design for Tissue/Time Specific Expression of Firefly Luciferase in Arabidopsis Plant Body

Name: RIKEN GenoCon

Affiliation: RIKEN The Institute of Physical and Chemical Research

Date: 2013-01-17

Abstract

PromoterCAD uses plant gene sequence and expression data to create synthetic promoters for tissue and time specific expression. The experimental test of such synthetic promoters will be to measure firefly Luciferase in Arabidopsis plant body. The program provides a graphical user interface (GUI), so anyone can design promoters using options in a series of select menus and push buttons. The program is written in JavaScript, on an open platform that allows for easy user customization. 


The program provides several plugin tools for promoter designs MotifExpress, and MotifCircadian function, as well as LocusSelect function for graph visualization of expression data. MotifExpress picks up the sequence motifs from the gene with maximum/minimum expression in a specific developmental condition or time of day. MotifCircadian picks up the motifs with maximum circadian amplitude. Output includes visualization such as HighCharts graph visualization of expression data under experimental conditions (AtGenExpress) and time evolution of expression under circadian conditions (DIURNAL). Programmers can easily fork and add to these functions following the PromoterCAD manuals and help pages:


For detail of GenoCon2 Promoter Design Challenge, please see the Promoter Design Challenge page. If you are ready to submit a design to GenoCon2, please check the manual for Promoter Design Submission. If you want to learn more about the PromoterCAD software and data, check out the PromoterCAD homepage.


jquery-1.7.1.min.js
jquery-ui-1.8.18.min.js
http://code.highcharts.com/highcharts.js
http://code.highcharts.com/modules/exporting.js


Contributor Send Message
Run count 859
Website
License
Fork count 6
Created date Dec 28, 2012
Last update date Jan 30, 2013

Forked (Child App)

forked:PromoterCAD Contributor: Kara_Tsukashima Update: Feb 26, 2013 19 runs
forked:PromoterCAD Contributor: Johan Update: Feb 23, 2013 42 runs
forked:PromoterCAD Contributor: Johan Update: Feb 23, 2013 16 runs
PromoterCAD Contributor: GenoCon Update: Feb 8, 2013 235 runs
forked:PromoterCAD Contributor: Koro_Nishikata Update: Jan 29, 2013 86 runs
PromoterCAD Beginning Tutorial 1 - example application Contributor: Koro_Nishikata Update: Jan 25, 2013 73 runs
  • LinkData work list used as input data in this application.
  • You can change input data and execute application if you change the checkbox.
  • Application Plugins for Synthetic Promoter Design Contributor: GenoCon Update: Feb 8, 2013
    40 Downloads
    [method]
  • [result_bottom]
    [result_top]
  • [AtGenExpress,ATTED,database,MotifExpress,LocusSelect,ManualInputMotif]
    [AtGenExpress,ATTED,database,MotifExpress,LocusSelect,ManualInputMotif]
    [AtGenExpress,ATTED,database,MotifExpress,LocusSelect,ManualInputMotif]
    [AtGenExpress,ATTED,database,MotifExpress,LocusSelect,ManualInputMotif]
    [AtGenExpress,ATTED,database,MotifExpress,LocusSelect,ManualInputMotif]
    [AtGenExpress,ATTED,database,MotifExpress,LocusSelect,ManualInputMotif]
    [AtGenExpress,ATTED,database,MotifExpress,LocusSelect,ManualInputMotif]
    [heptamer]
  • [result_top]
    [result_top]
    [result_top]
    [result_top]
    [result_top]
    [result_top]
    [result_bottom]
    [result_top]
  • PPDB promoter sequence Contributor: Koro_Nishikata Update: Jan 17, 2013
    24 Downloads
    [ppdb_baseLineSequence]
  • Circadian Genomic (DIURNAL + PPDB promoter motif) Full Contributor: GenoCon Update: Jan 15, 2013
    512 Downloads
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,PPDB,database,MotifExpress,LocusSelect,MotifCircadian]
  • Tooltip information Contributor: Koro_Nishikata Update: Feb 5, 2013
    54 Downloads
    [tooltip]
    [tooltip]
    [tooltip]
  • Circadian Coexpression (DIURNAL + ATTED-II promoter motif) Full Contributor: GenoCon Update: Jan 15, 2013
    491 Downloads
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
    [DiurnalHours,ATTED,database,MotifExpress,LocusSelect,MotifCircadian]
  • Speedup Lists of Circadian Genomic (DIURNAL + PPDB promoter motif) Gene Contributor: GenoCon Update: Jan 15, 2013
    248 Downloads
    [result_top]
    [result_top]
    [result_top]
    [result_top]
    [result_top]
    [result_top]
    [result_bottom]
    [result_top]
  • ATTED promoter sequence Contributor: Koro_Nishikata Update: Jan 15, 2013
    27 Downloads
    [atted_baseLineSequence]
  • [result_bottom]
    [result_top]
  • Developmental Genomic (AtGenExpress + PPDB promoter motif) Full Contributor: GenoCon Update: Jan 22, 2013
    227 Downloads
    [AtGenExpress,PPDB,database,MotifExpress,LocusSelect]
    [AtGenExpress,PPDB,database,MotifExpress,LocusSelect]
    [AtGenExpress,PPDB,database,MotifExpress,LocusSelect]
    [AtGenExpress,PPDB,database,MotifExpress,LocusSelect]
    [AtGenExpress,PPDB,database,MotifExpress,LocusSelect]
    [AtGenExpress,PPDB,database,MotifExpress,LocusSelect]
    [AtGenExpress,PPDB,database,MotifExpress,LocusSelect]
    [octamer]
  • Add New Data

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