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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/tutorial/ppt/WebQTLDemo_files/slide0059.htm
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
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+</script> <meta name=Description content="Jun-19-03: Requirement: The gene must be polymorphic to be genetically ÒupstreamÓ"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 &#1;";mso-line-spacing:" 0 &#1;"'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-size:82%'><i>Requirement: The gene must be polymorphic to </i></span></span></layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-size:82%'><i>be genetically ÒupstreamÓ</i></span><span style='font-size:82%;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App and many other<br> </i></span></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>correlated transcripts and </i></span></span></layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</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><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-21 15:14:01 +0000