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This presentation shows the steps for someone who is
interested in finding both the sequence level promoter motifs
of yeast genes plus the transcription factors that
regulate their expression.
If a researcher is interested in ultimately finding networks
regulation but first wants to check specific favorite genes
of interest, then he can follow these steps.
Start by opening the website of Yeastract--
ww.yeastract.com.
A window will appear with an introduction
to associated tools.
Also, several options are given in blue on the left-hand
side of the window.
These will be used in this tutorial.
When clicking on them, they'll change the color into purple
as a reminder to which options have been used.
For example, click on Search for TFs, or transcription
factors, under Regulatory Associations in the left-hand
column of the home page.
Now, a window will open where you can type your sequence ID
or name, like, for example, cdc24.
Click Search to get the transcription factor, TF.
You can make a choice between showing only documented, only
potential, or both documented and potential
transcription factors.
Under Documented Regulations, one can also choose between
Direct and/or Indirect Evidence.
When you make the choice to show in documented or
potential transcription factors, the option is given
to show a color figure in image.
Consider the options given, and, if necessary, go a few
steps back to redo the search.
If you're satisfied with the given options, then
go to the next step.
Now, in the table, click on the transcription factor of
interest, like, for example, Abf1p at position -165.
And go to the next step to consider the motifs found to
which this transcription factor binds.
From this window, either copy one of the transcription
factor binding sites or go to the next step.
If necessary for further study of motifs of this gene's
upstream sequence, from this window, either copy the FASTA
sequence or resume the previous step.
Clicking on the binding site will give
the literature reference.
From this window, copy the transcription factor binding
site and go to the next step.
On the left side of the window, click on Search by DNA
Motif and paste the copied motif into the below window
described as Search Described TF Binding Sites
by Given DNA Motif.
After pasting the copied motif into the below window, click
on the Search button to search for described transcription
factor binding sites given by this particular DNA motif.
In the window that now appears, search for other
described transcription factor binding sites by
the given DNA motifs.
Click on one of the options given--
like for example, Grc1p.
And, if necessary, repeat the same steps.
Now consider all the other options and try the different
alternatives as given by the websites to try and find
transcription factor binding sites.