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genomics</title>
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mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Physical
map for distal chromosome 7</span><span style='font-family:Verdana;font-size:
73%;mso-special-format:lastCR;display:none'><i><br>
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mso-text-raise:0%'><span style='font-size:167%;color:#E9EB5D'>Distal Chr 7 from
~120 and 132 Mb may modulate</span><span style='font-size:167%;color:#E9EB5D'><i>
App</i></span><span style='font-size:200%;color:#E9EB5D;mso-special-format:
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<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Physical map of variation
in App expression in brain on distal Chr 7 (a blow up of the whole-genome
map on the previous slide).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
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<td align=left colspan=1><font face=Verdana size=3>Notes:</font><br>
</td>
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<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Verdana size=3> You can now see that the X-axis is on a physical scale
of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br>
</td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. The small irregular
colored blocks and marks toward the top of the map mark the locations of
genes superimposed on the physical map. Neighboring genes are offset
slightly in the vertical axis for display purpose. Note one region of very
high gene density from about 120 to 123 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. The orange hash marks
along the X-axis represent the number of single nucleotide polymorphisms
that distinguish the two parental strains (C57BL/6J and DBA/2J) from each
other. We call this the SNP seismograph track (see Glossary for more
details). Regions with low numbers of SNP have closely matched sequences and
are less likely to contain QTLs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4. As before, the thin
red line shows the additive effect size. By convention the positive values
signify the D alleles are associated with higher expression of App in this
region of Chr 7 than the B alleles. The maximum effect size is about +0.20
log2 expression units per D allele. The differences been the BB and DD
genotypes (BB and DD because each strain has two alleles; one per
chromosome) is therefore about 2^0.4 = 1.32; or a 32% increment in DD
relative to BB at this locus.</font><br>
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<td align=left colspan=1><font face=Verdana size=3>5. If you scroll just
under the Physical Map you will see text that reads �DISPLAY from XXX Mb TO
YYY Mb�..�<span style="mso-spacerun: yes"> </span>These physical maps
are zoomable, a feature we will exploit to evaluate candidate genes in this
QTL interval.</font><br>
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