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<meta name=Description content="Aug-15-05: Physical map for distal chromosome 7">
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mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%;
height:75.51%'><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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<div class=O style='position:absolute;top:11.42%;left:1.12%;width:98.87%;
height:74.28%'><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:
lastCR;display:none'><i><br>
</i></span></div>
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<tr>
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<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>
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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>
</tr>
<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 SNPs 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>
</td>
</tr>
<tr>
<td colspan=1></td>
<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 ÒDISPLAY from XXX Mb TO
YYY MbÉ..Ó<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>
</td>
</tr>
</table>
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