Difference between revisions of "Promoter Analysis"
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It should be noted that in general, the discovery of functional transcription factor binding sites involves biological experimentation, as the motifs are short and relatively common. This tool is a means of visualizing and testing hypotheses. | It should be noted that in general, the discovery of functional transcription factor binding sites involves biological experimentation, as the motifs are short and relatively common. This tool is a means of visualizing and testing hypotheses. | ||
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==Setting up== | ==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". | # Go to the '''Promoter''' component. Scroll through the list of available Transcription Factor binding site motifs. Here we will select "TBP:TATA-BOX:MA0108". | ||
# Double click on "TBP:TATA-BOX:MA0108" to add it to the search window just below. | # Double click on "TBP:TATA-BOX:MA0108" to add it to the search window just below. | ||
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| − | + | The Parameters tab: | |
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| − | + | [[Image:T_Promoter_Parameters.png]] | |
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| + | |||
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| + | The Sequence tab: | ||
| − | [[Image: | + | [[Image:T_Promoter_Sequence.png]] |
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| − | + | ==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. | ||
Revision as of 18:32, 13 August 2008
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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.
- View the results superimposed on the seqeunces.
- View statistics on the scan results.
Overview
The Promoter Component allows a set of sequences to be scanned by selected motifs of known transcription factor binding sites. These motifs are derived from the Jasper project. The motifs are in the form of PSSM - Position Specific Scoring Matices.
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 involves biological experimentation, as the motifs are short and relatively common. This tool is a means of visualizing and testing hypotheses.
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".
- Double click on "TBP:TATA-BOX:MA0108" to add it to the search window just below.
We can view the motif by selecting 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.
