geWorkbench

Outline

In this tutorial, we will

1. Select a transcription factor motif to scan against a set of sequences.
2. Run the scan.
3. View the results superimposed on the seqeunces.
4. 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.

We will use a set of 64 sequences belonging to genes selected as being part of a distintive group found through Hierarchical Clustering. Such a cluster could be interogated as whether particular TFs are overreprsented or are present in some common pattern.

Setting up

1. In the Project Folders component, if the sequences are not already present, open the file "640f84ClusterPearsonsSeqs.fasta", available as part of the tutorials download file.
2. Go to the Promoter component. Scroll through the list of available Transcription Factor binding site motifs. Here we will select "TBP:TATA-BOX:MA0108".
3. 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:

Running and viewing the scan

1. Hit Scan.
2. Check the box "Show TFs".
3. Hits of this motif against the sequences are displayed in the sequence window at right.

Viewing statistics about the search results

Statistics for the hits are shown on the Parameters tab. Here we see that the motif occurs at a higher frequency than predicted by chance.