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forked:new PromoterCAD + MotifRanking

PromoterCADの新バージョンに拙作のMotifRankingプラグインを移植しました。
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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
Forked from (Parent App) Masahiro Mochizuki 's new PromoterCAD + MotifRanking
Run count 52
Website
License
Fork count 0
Created date Feb 26, 2013
Last update date Feb 26, 2013

Forked from (Parent App)

new PromoterCAD + MotifRanking Contributor: Masahiro Mochizuki Update: Feb 11, 2013 385 runs
  • LinkData work list used as input data in this application.
  • You can change input data and execute application if you change the checkbox.
  • PromoterCAD plugin tools Contributor: GenoCon Update: Mar 8, 2013
    99 Downloads
    [method]
  • PromoterCAD Data Tables Contributor: Koro_Nishikata Update: Mar 7, 2013
    49 Downloads
    [menu]
  • [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]
  • Circadian Genomic (DIURNAL + PPDB promoter motif) Full Contributor: GenoCon Update: Jan 15, 2013
    2244 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]
  • Circadian Coexpression (DIURNAL + ATTED-II promoter motif) Full Contributor: GenoCon Update: Jan 15, 2013
    2335 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
    1266 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
    83 Downloads
    [atted_baseLineSequence]
  • [result_bottom]
    [result_top]
  • PromoterCAD_tooltips Contributor: Koro_Nishikata Update: May 16, 2013
    292 Downloads
    [tooltip]
    [tooltip]
    [tooltip]
  • Data for New Promoter CAD App Contributor: Masahiro Mochizuki Update: Feb 26, 2013
    212 Downloads
    [method]
    [menu]
    [tooltip]
  • [result_bottom]
    [result_top]
  • [result_top]
    [result_top]
    [result_top]
    [result_top]
    [result_top]
    [result_top]
    [result_bottom]
  • PPDB promoter sequence Contributor: Koro_Nishikata Update: Jan 17, 2013
    78 Downloads
    [ppdb_baseLineSequence]
  • Developmental Genomic (AtGenExpress + PPDB promoter motif) Full Contributor: GenoCon Update: Jan 22, 2013
    1029 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]
    [method]
  • Add New Data

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