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must be polymorphic to </i></span></span></layer><script>
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style='text-align:left'><span style='font-size:82%'><i>be genetically
�upstream�</i></span><span style='font-size:82%;mso-special-format:lastCR;
display:none'><br>
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style='font-size:64%'><i>What are targets of the Hars2 polymorphisms?</i></span><span
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<div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App
and many other<br>
</i></span></div>
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%;
color:#E9EB5D'><i>correlated transcripts and </i></span></span></layer><script>
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%;
color:#E9EB5D'><i>other traits.</i></span></span></layer></div>
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<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Genes must be polymorphic
to generate downstream genetic effects (as opposed to downstream molecular
effects). Hars2 meets this condition because we have already mapped a
functional polymorphism in the gene. We can therefore posit that Hars2 is a
QT gene. What transcripts are downstream? <i>App</i> is one obvious
candidate, but there are many more.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The are several ways to
look for downstream targets. The best and most obvious is to look up all
transcripts that have high correlations with Hars2 itself. You should know
how to do this. An alternative method is shown here for teaching purpose and
to show you what to do if your gene of interest is not in our database. You
need to know:</font><br>
</td>
</tr>
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<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
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<td colspan=1></td>
<td align=left colspan=1><font face=Times size=3>1.</font><font
face=Verdana size=3> Where your gene is located. You need this information
to find a surrogate marker; a marker that is located very close to your gene
of interest.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. That your gene is
polymorphic between C57BL/6J and DBA/2J.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Let�s look at the
correlation of Hars2 with BXD genotypes as shown in the slide above to
illustrate how to use markers as surrogate traits.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Go to the Trait Date and
Editing window one more time. We want the data for Hars2 this time, not App.
You should be able to show that Hars2 has a high<span style="mso-spacerun:
yes"> </span>correlation with D2Mit423 as shown in the slide above.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>By clicking on the symbol
D2Mit423 in the Correlation window, you will generate a new Trait Data
window shown on the next slide.</font><br>
</td>
</tr>
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