Finding Common Transcription Factor Binding Motifs for Multiple Genes

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– 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.

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