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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/tutorial/ppt/WebQTLDemo_files/slide0059.htm
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
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-</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>other traits.</i></span></span></layer></div> </layer></div> </LAYER>
- <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <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> <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=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>LetÕs 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">&nbsp; </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> </table> </div> </layer> <script language=JavaScript><!--
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generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 22:59:17 +0000