Difference between revisions of "Promoter Analysis"
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==Overview== | ==Overview== | ||
| − | The Promoter | + | The '''Promoter''' component scans one or more sequence motifs against user supplied nucleotide sequence(s). Motifs from the JASPAR database of transcription factor binding sites are included with the component. Additional motifs can be added by the user. |
The '''Promoter''' component will also display the results of hits found in the '''Pattern Discovery''' component. | The '''Promoter''' component will also display the results of hits found in the '''Pattern Discovery''' component. | ||
| − | It should be noted that in general, the discovery of functional transcription factor binding sites | + | It should be noted that in general, the discovery of functional transcription factor binding sites includes biological experimentation, as the motifs are short and relatively common. This tool is a means of visualizing and testing hypotheses. |
| + | ==JASPAR== | ||
| + | |||
| + | The motif datafile currently included with geWorkbench is version 3.0 of the JASPAR CORE database ([http://jaspar.genereg.net/ http://jaspar.genereg.net/]) . It contains 138 curated, non-redundant profiles. These "profiles are derived from published collections of experimentally defined transcription factor binding sites for multi-cellular eukaryotes. The database represents a curated collection of target sequences" ([http://jaspar.genereg.net/html/TEMPLATES/help.html http://jaspar.genereg.net/html/TEMPLATES/help.html]). | ||
| + | |||
| + | The profiles are represented by counts of how many times each of the four nucleotide bases occurs at a particular position in the aligned sequences. | ||
==Setting up== | ==Setting up== | ||
Revision as of 15:20, 12 October 2009
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Outline
In this tutorial, we will
- Select a transcription factor motif to scan against a set of sequences.
- Run the scan.
Overview
The Promoter component scans one or more sequence motifs against user supplied nucleotide sequence(s). Motifs from the JASPAR database of transcription factor binding sites are included with the component. Additional motifs can be added by the user.
The Promoter component will also display the results of hits found in the Pattern Discovery component.
It should be noted that in general, the discovery of functional transcription factor binding sites includes biological experimentation, as the motifs are short and relatively common. This tool is a means of visualizing and testing hypotheses.
JASPAR
The motif datafile currently included with geWorkbench is version 3.0 of the JASPAR CORE database (http://jaspar.genereg.net/) . It contains 138 curated, non-redundant profiles. These "profiles are derived from published collections of experimentally defined transcription factor binding sites for multi-cellular eukaryotes. The database represents a curated collection of target sequences" (http://jaspar.genereg.net/html/TEMPLATES/help.html).
The profiles are represented by counts of how many times each of the four nucleotide bases occurs at a particular position in the aligned sequences.
Setting up
- Load a set of nucleotide sequences of interest.
- Go to the Promoter component. Scroll through the list of available Transcription Factor binding site motifs. Here we will select "TBP:TATA-box:MA0108".
The motif is graphically depicted on the "Logo" tab:
The Parameters tab:
The Sequence tab:
Running and viewing the scan
- Hit Scan.
- Check the box "Show TFs".
- Hits of this motif against the sequences are displayed in the sequence window.
