web/tutorial/ppt/WebQTLDemo_files/slide0041.htm


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   <td colspan=1></td>
   <td align=left colspan=1><font face=Helvetica size=3>Many of the data types
   in the previous slide are hot-linked and it is easy to generate a small web
   of correlations between any transcript of interest and many other
   transcripts. In this case, we have used green lines between transcripts that
   have positive correlations, and red lines between transcripts that have
   negative correlations. Correlations have been multiplied by 100. The
   correlation of 0.96 between App and Hsp84-1 reads 96.<span
   style="mso-spacerun: yes">&nbsp; </span>These are Pearson product moment
   correlations and they are sensitive to outliers. If you prefer, you can
   recompute Spearman rank order correlations.</font><br>
   </td>
  </tr>
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   <td align=left colspan=1><br>
   </td>
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   <td align=left colspan=1><font face=Helvetica size=3>Where did Ndr4 (lower
   left) come from? It is not in the list in the previous slide. Actually it
   is. Nomenclature changes rapidly. If you click on R74996 in the previous
   slide (the active webqtl version) you will see that it now has a new symbol
   and name.</font><br>
   </td>
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   <td align=left colspan=1><br>
   </td>
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   <td align=left colspan=1><font face=Helvetica size=3>What are all of
   the<span style="mso-spacerun: yes">&nbsp; </span>conventions in this
   correlation network sketch.</font><br>
   </td>
  </tr>
  <tr>
   <td colspan=1></td>
   <td align=left colspan=1><font face=Times size=3>1.</font><font
   face=Helvetica size=3>The official gene symbol = App</font><br>
   </td>
  </tr>
  <tr>
   <td colspan=1></td>
   <td align=left colspan=1><font face=Helvetica size=3>2. OUr estimate of the
   location of these gene in the Mouse Genome Sequencing Consoritum version 3
   build (MGSCv3). Chromosome followed by the megabase position relative to the
   centromere. (Mice only have one chromosome arm so this is an unambiguous
   coordinate. )</font><br>
   </td>
  </tr>
  <tr>
   <td colspan=1></td>
   <td align=left colspan=1><font face=Helvetica size=3>3. The pair of numbers:
   top is the highest expression among the strain set. The lower number is the
   lowest expression of that transcript among the strain set.</font><br>
   </td>
  </tr>
  <tr>
   <td colspan=1></td>
   <td align=left colspan=1><font face=Helvetica size=3>4. Vertical number on
   the right side of each box: this is the probe set ID given by Affymetrix. We
   have truncated these probe set IDs so you will not see the usual<span
   style="mso-spacerun: yes">&nbsp; </span>�at�. A single gene may be
   represented by more than 10 probe sets. Thus this ID number is essential to
   identify the actual data source.</font><br>
   </td>
  </tr>
  <tr>
   <td colspan=1></td>
   <td align=left colspan=1><font face=Helvetica size=3>5. Lower right corner:
   a two digit number followed by plus and minus signs. These numbers are the
   correlation value (absolute value) of the 100th best correlated transcript.
   The plus and minus signs indicate the mean polarity of the correlations.</font><br>
   </td>
  </tr>
  <tr>
   <td colspan=1></td>
   <td align=left colspan=1><font face=Helvetica size=3>6. The set of numbers
   that read 2@140* etc. These are the approximate locations of additive effect
   QTLs detected by WebQTL that we will describe in other slides. Read this as:
   App has a suggestive QTL on Chr 2 at about 140 Mb and the D allele inherited
   from DBA/2J confirms a higher expression level at this marker.<span
   style="mso-spacerun: yes">&nbsp; </span>If there is no star symbol, then it
   is not even formally �suggestive� but does make an interesting looking blip
   on the QTL radar screen.</font><br>
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