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<title>PowerPoint Presentation  -  Complex trait analysis, develop-ment, and
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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  <tr>
   <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>
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   <td colspan=1></td>
   <td align=left colspan=1><br>
   </td>
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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>
  </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 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>
   </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 �DISPLAY from XXX Mb TO
   YYY Mb�..�<span style="mso-spacerun: yes">&nbsp; </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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