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Application Information

PromoterCAD: Data Driven Design of Plant Regulatory DNA

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.


PromoterCAD web page:
http://promotercad.org/
Manuals for PromoterCAD:
http://promotercad.org/manuals/

License

The source code for PromoterCAD is now licensed under the LGPL-3.0 license (the GNU Lesser General Public License, version 3.0) and the Creative Commons license CC-BY-SA, which allows for unlimited reuse and modification of the source code. Users can select either one of the licenses LGPL-3.0 and CC-BY-SA, when using the source code. Any users can access the source code of this application as follows.
http://app.linkdata.org/update/app1s335i

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Tooltip

To facilitate the usability of PromoterCAD, we provide the tooltip informartion. Then it is easy for users to undergo the promoter motif manipulation.

Hover the cursor to the items such as the button "Start promoter design", and the PromoterCAD returns the messsage
"Start your promoter design with the empty sequence in the region -51 to -550 from the transcriptional start site."

Then users can start their promoter design by clicking the button.

Basic Usage

To execute the synthetic promoter design using the PromoterCAD, please go through the following workflow basically.

  1. At first, with the menu "Select tool", users can select one of the functions for performing a particular data operation. For example, the function "MotifMaxExpress" finds motifs associated with maximum gene expression in a specific condition. Select this function to find motifs associated with strong expression in flower tissues.
  2. With the menu "Analysis Method", users can select a regulatory motif data set (ATTED/PPDB) registered in LinkData.
  3. With the menu "Expression Database", users can select microarray expression database (AtGenExpress/DIURNAL) registered in LinkData. Data containing the developmental series from AtGeneExpress has been split into a series of data tables by tissue type, and those from DIURNAL has been split into a a series of data tables by circadian growth condition.
  4. With the menu "Data Collection", users can select the data tables corresponding to the interesting developmental/circadian condition. (e.g. "Flowering")
  5. The next menu "Select Property", users can select one of the expression conditions associated with the database. For the AtGenExpress data, this is represented by a shorthand description. For example, "Col-0_flower" refers to the Columbia strain 0, grown for 4 weeks until the flowering stage. The gene expression levels are for the entire flower.
    The full description of each experiment can be referenced on the TAIR website. For example, flowering experiments are described here:
    http://arabidopsis.org/servlets/TairObject?type=bio_sample_collection&id=1006710 873#437
    Select a particular experiment and MotifExpress will find known sequence motifs associated with high expression in this condition. MotifMaxExpress will automatically display these motif sequences (in this case septamers) in line with the base promoter sequence at the same location as they occur in the promoter returned by MotifExpress.
  6. By clicking the button "Add motif", all the selected motifs are incorporated into the promoter motif skelton. The result will be displayed in the text area with the motifs indicated by color.
  7. Click the button "Next", to repeat the sequence design operation and continue the workflow. (Continues the steps 1-6.)
  8. In the final step, click the button "Finish Now" to fill in the skeleton (the 'bones' of the promoter, containing just regulatory motifs and the minimal promoter region) with the remaining sequence. This will replace the blank '-' sequences, but will preserve any motifs added in the design process.

Tutorials

Here are tutorials to execute synthetic promoter designs using PromoterCAD. These have example walk throughs with snapshots for each step.

Beginning_Tutorials_1 This tutorial illustrates how to design a synthetic promoter for Leaf specific expression using the MotifExpress tool.
Beginning_Tutorials_2 This tutorial illustrates how to design a synthetic promoter for Circadian expression with MotifCircadian tool.
Beginning_Tutorials_3 This tutorial illustrates how to use InputMotif tool to add specific motifs to a gene design.
Advanced_Tutorials_1 This tutorial illustrates how to fork your own PromoterCAD workspace.
Advanced_Tutorials_2A This tutorial illustrates how to add a new normalized data to PromoterCAD.
Advanced_Tutorials_2B This tutorial illustrates how to add a new database PLACE motif data to PromoterCAD.
Advanced_Tutorials_3A This tutorial illustrates how to add a new data mining plugin tool MotifRanking.
Advanced_Tutorials_3B This tutorial illustrates how to add a new data mining plugin tool MotifNonCircadian.
Advanced_Tutorials_4 This tutorial illustrates how to modify and upload your own tooltips.
Help Page Interpreting PromoterCAD Output
Help Page How to tag input LinkData tables for PromoterCAD

License

PromoterCAD source code is licensed under the LGPL-3.0 license (the GNU Lesser General Public License, version 3.0) and the Creative Commons license CC-BY-SA. So users can fork the source code of PromoterCAD to easily create their own data mining plugins.


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
http://code.highcharts.com/highcharts-more.js


Contributor Send Message
Forked from (Parent App) GenoCon 's PromoterCAD
Run count 1846
Website
License
Fork count 4
Created date Apr 26, 2013
Last update date May 16, 2013

Forked from (Parent App)

PromoterCAD Contributor: GenoCon Update: Apr 28, 2013 333 runs

Forked (Child App)

forked:PromoterCAD: Data Driven Design of Plant Regulatory DNA Contributor: Robert Cox Update: Jun 6, 2013 69 runs
PromoterCAD + MotifRanking Contributor: GenoCon Update: May 16, 2013 103 runs
PromoterCAD Beginning Tutorial 1 - example application Contributor: Koro_Nishikata Update: May 16, 2013 205 runs
forked:PromoterCAD - example application for advanced tutorials Contributor: Koro_Nishikata Update: May 16, 2013 113 runs
  • LinkData work list used as input data in this application.
  • You can change input data and execute application if you change the checkbox.

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