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<td width=100% id="p10" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('10')" id=AREF>"What a network is
likely..."</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p11" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('11')" id=AREF>Are there experimental
results to corroborate a link between App with Hsp84-1?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p12" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('12')" id=AREF>"2.45 billion scatter
plots"</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p13" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('13')" id=AREF>"Cross-tissue type
correlations"</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p14" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('14')" id=AREF>"Cross-modal
correlations:"</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID15 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p15" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('15')" id=AREF>WebQTL<span
style="mso-spacerun: yes"> </span><br>
link to <br>
www.webqtl.org/search.html</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID16 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p16" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('16')" id=AREF>Slide 16</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID17 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p17" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('17')" id=AREF>Slide 17</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID18 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p18" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('18')" id=AREF>WebQTL to exploring
upstream control</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID19 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p19" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('19')" id=AREF>WebQTL to exploring
upstream control.</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID20 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p20" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('20')" id=AREF>The whole neighborhood is
modulated!</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID21 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p21" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('21')" id=AREF>Which gene is the QTL?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID22 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p22" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('22')" id=AREF>Slide 22</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID23 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p23" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('23')" id=AREF>Slide 23</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID24 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p24" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('24')" id=AREF>Tissue differences in probe
performance</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID25 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p25" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('25')" id=AREF>Is there known biology to
link Hars2 with App?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID26 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p26" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('26')" id=AREF>WebQTL<span
style="mso-spacerun: yes"> </span><br>
link to <br>
www.webqtl.org/search.html</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID27 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p27" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('27')" id=AREF>Requirement: The gene must
be polymorphic to be genetically ÒupstreamÓ</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID28 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p28" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('28')" id=AREF>Direct correlations between
genotypes and traits</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID29 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p29" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('29')" id=AREF>WhatÕs downstream of Chr 2
near Hars2?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID30 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p30" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('30')" id=AREF>WhatÕs downstream of Chr 2
near Hars2?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID31 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p31" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('31')" id=AREF>Does Hars2 correlate with
Actn2 strongly?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID32 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p32" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('32')" id=AREF>Contact for comments and
improvements:</a></b></font></td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/outline_expand.gif b/web/tutorial/ppt/WebQTLDemo_files/outline_expand.gif Binary files differdeleted file mode 100755 index c8c72b13..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/outline_expand.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm b/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm deleted file mode 100755 index 3e6bdf31..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Robots content=NoIndex>
<style>
<!--a {text-decoration: none;}-->
</style>
</head>
<body bgcolor=black text=white link=white vlink=white alink=white
onload=" parent.base.highlite();" onresize="self.location.reload();">
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p1" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('1')" id=AREF>WebQTL Demonstration
One<br>
please link to <br>
www.webqtl.org/search.html</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Part 1: How to discover shared
expression patterns (slides 2Ð14)</font></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators
(15Ð25)</font></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Discovering downstream targets</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p2" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('2')" id=AREF>"or
webqtl.org/search.html..."</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>or webqtl.org/search.html (mirror)</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p3" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('3')" id=AREF>Search results</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p4" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('4')" id=AREF>"First page of data:"</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>First page of data: The ÒTrait Data
FormÓ</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p5" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('5')" id=AREF>"Data sources:"</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Data sources: Phenotpyes and genotypes</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p6" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('6')" id=AREF>"Return to Trait Data
page"</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Return to Trait Data page</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p7" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('7')" id=AREF>"Discovering shared
expression patterns"</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Discovering shared expression patterns</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p8" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('8')" id=AREF>"The App transcript
neighborhood"</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>The App transcript neighborhood</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p9" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('9')" id=AREF>"Handdrawn sketch of
the neighborhood"</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Handdrawn sketch of the neighborhood</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p10" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('10')" id=AREF>"What a network is
likely..."</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>What a network is likely to look like
(but App will not be center of universe).</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p11" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('11')" id=AREF>Are there experimental
results to corroborate a link between App with Hsp84-1?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p12" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('12')" id=AREF>"2.45 billion scatter
plots"</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>2.45 billion scatter plots: here is one
of the best</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p13" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('13')" id=AREF>"Cross-tissue type
correlations"</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Cross-tissue type correlations</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p14" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('14')" id=AREF>"Cross-modal
correlations:"</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Cross-modal correlations: From mRNA to
to anatomy and to behavior and pharmacology</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID15 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p15" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('15')" id=AREF>WebQTL<span
style="mso-spacerun: yes"> </span><br>
link to <br>
www.webqtl.org/search.html</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Discovering shared expression patterns</font></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Discovering upstream modulators (QTLs)</font></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Discovering downstream targets</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID16 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p16" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('16')" id=AREF>Slide 16</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID17 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p17" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('17')" id=AREF>Slide 17</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID18 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p18" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('18')" id=AREF>WebQTL to exploring
upstream control</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID19 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p19" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('19')" id=AREF>WebQTL to exploring
upstream control.</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID20 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p20" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('20')" id=AREF>The whole neighborhood is
modulated!</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID21 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p21" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('21')" id=AREF>Which gene is the QTL?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID22 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p22" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('22')" id=AREF>Slide 22</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID23 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p23" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('23')" id=AREF>Slide 23</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID24 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p24" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('24')" id=AREF>Tissue differences in probe
performance</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID25 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p25" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('25')" id=AREF>Is there known biology to
link Hars2 with App?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID26 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p26" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('26')" id=AREF>WebQTL<span
style="mso-spacerun: yes"> </span><br>
link to <br>
www.webqtl.org/search.html</a></b></font></td>
</tr>
</table>
<table>
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Discovering shared expression patterns</font></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Discovering upstream modulators (QTLs)</font></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Discovering downstream targets</font></td>
</tr>
</table>
<br>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID27 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p27" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('27')" id=AREF>Requirement: The gene must
be polymorphic to be genetically ÒupstreamÓ</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID28 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p28" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('28')" id=AREF>Direct correlations between
genotypes and traits</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID29 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p29" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('29')" id=AREF>WhatÕs downstream of Chr 2
near Hars2?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID30 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p30" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('30')" id=AREF>WhatÕs downstream of Chr 2
near Hars2?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID31 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p31" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('31')" id=AREF>Does Hars2 correlate with
Actn2 strongly?</a></b></font></td>
</tr>
</table>
<table width=100%>
<tr>
<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID32 VISIBILITY=hidden >></ilayer>'); } </script></td>
<td width=100% id="p32" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('32')" id=AREF>Contact for comments and
improvements:</a></b></font></td>
</tr>
</table>
</body>
</html>
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- new hrefList("slide0032.htm", 1, 32)
-);
- -function ImgBtn( oId,bId,w,action ) -{ - var t=this - t.Perform = _IBP - t.SetActive = _IBSetA - t.SetInactive= _IBSetI - t.SetPressed = _IBSetP - t.SetDisabled= _IBSetD - t.Enabled = _IBSetE - t.ChangeIcon = null - t.UserAction = action - t.ChgState = _IBUI - t.mObjId = oId - t.mBorderId= bId - t.mWidth = w - t.mIsOn = t.mCurState = 0 -} -function _IBSetA() -{ - if( this.mIsOn ) { - obj=this.ChgState( gHiliteClr,gShadowClr,2 ) - obj.style.posTop=0 - } -} -function _IBSetI() -{ - if( this.mIsOn ) { - obj=this.ChgState( gFaceClr,gFaceClr,1 ) - obj.style.posTop=0 - } -} -function _IBSetP() -{ - if( this.mIsOn ) { - obj=this.ChgState( gShadowClr,gHiliteClr,2 ) - obj.style.posLeft+=1; obj.style.posTop+=1 - } -} -function _IBSetD() -{ - obj=this.ChgState( gFaceClr,gFaceClr,0 ) - obj.style.posTop=0 -} -function _IBSetE( state ) -{ - var t=this - GetObj( t.mBorderId ).style.visibility="visible" - if( state != t.mIsOn ) { - t.mIsOn=state - if( state ) - t.SetInactive() - else - t.SetDisabled() - } -} -function _IBP() -{ - var t=this - if( t.mIsOn ) { - if( t.UserAction != null ) - t.UserAction() - if( t.ChangeIcon ) { - obj=GetObj(t.mObjId) - if( t.ChangeIcon() ) - obj.style.posLeft=obj.style.posLeft+(t.mCurState-4)*t.mWidth - else - obj.style.posLeft=obj.style.posLeft+(t.mCurState-0)*t.mWidth - } - t.SetActive() - } -} -function _IBUI( clr1,clr2,nextState ) -{ - var t=this - SetBorder( GetObj( t.mBorderId ),clr1,clr2 ) - obj=GetObj( t.mObjId ) - obj.style.posLeft=obj.style.posLeft+(t.mCurState-nextState)*t.mWidth-obj.style.posTop - t.mCurState=nextState - return obj -} -function TxtBtn( oId,oeId,action,chkState ) -{ - var t=this - t.Perform = _TBP - t.SetActive = _TBSetA - t.SetInactive= _TBSetI - t.SetPressed = _TBSetP - t.SetDisabled= _TBSetD - t.SetEnabled = _TBSetE - t.GetState = chkState - t.UserAction = action - t.ChgState = _TBUI - t.mObjId = oId - t.m_elementsId= oeId - t.mIsOn = 1 -} -function _TBSetA() -{ - var t=this - if( t.mIsOn && !t.GetState() ) - t.ChgState( gHiliteClr,gShadowClr,0,0 ) -} -function _TBSetI() -{ - var t=this - if( t.mIsOn && !t.GetState() ) - t.ChgState( gFaceClr,gFaceClr,0,0 ) -} -function _TBSetP() -{ - if( this.mIsOn ) - this.ChgState( gShadowClr,gHiliteClr,1,1 ) -} -function _TBSetD() -{ - this.ChgState( gFaceClr,gFaceClr,0,0 ) - this.mIsOn = 0 -} -function _TBSetE() -{ - var t=this - if( !t.GetState() ) - t.ChgState( gFaceClr,gFaceClr,0,0 ) - else - t.ChgState( gShadowClr,gHiliteClr,1,1 ) - t.mIsOn = 1 -} -function _TBP() -{ - var t=this - if( t.mIsOn ) { - if( t.UserAction != null ) - t.UserAction() - if( t.GetState() ) - t.SetPressed() - else - t.SetActive() - } -} -function _TBUI( clr1,clr2,lOffset,tOffset ) -{ - SetBorder( GetObj( this.mObjId ),clr1,clr2 ) - Offset( GetObj( this.m_elementsId ),lOffset,tOffset ) -} -function GetObj( objId ){ return document.all.item( objId ) } -function Offset( obj, top, left ){ obj.style.top=top; obj.style.left=left } -function SetBorder( obj, upperLeft, lowerRight ) -{ - s=obj.style; - s.borderStyle = "solid" - s.borderWidth = 1 - s.borderLeftColor = s.borderTopColor = upperLeft - s.borderBottomColor= s.borderRightColor = lowerRight -} -function GetBtnObj(){ return gBtnArr[window.event.srcElement.id] } -function BtnOnOver(){ b=GetBtnObj(); if( b != null ) b.SetActive() } -function BtnOnDown(){ b=GetBtnObj(); if( b != null ) b.SetPressed() } -function BtnOnOut(){ b=GetBtnObj(); if( b != null ) b.SetInactive() } -function BtnOnUp() -{ - b=GetBtnObj() - if( b != null ) - b.Perform() - else - Upd() -} -function GetNtsState(){ return parent.gNtsOpen } -function GetOtlState(){ return parent.gOtlOpen } -function GetOtlTxtState(){ return parent.gOtlTxtExp } -function NtsBtnSetFlag( fVal ) -{ - s=document.all.item( this.m_flagId ).style - s.display="none" - if( fVal ) - s.display="" - else - s.display="none" -} - -var gHiliteClr="THREEDHIGHLIGHT",gShadowClr="THREEDSHADOW",gFaceClr="THREEDFACE" -var gBtnArr = new Array() -gBtnArr["nb_otl"] = new TxtBtn( "nb_otl","nb_otlElem",parent.ToggleOtlPane,GetOtlState ) -gBtnArr["nb_nts"] = new TxtBtn( "nb_nts","nb_ntsElem",parent.ToggleNtsPane,GetNtsState ) -gBtnArr["nb_prev"]= new ImgBtn( "nb_prev","nb_prevBorder",30,parent.GoToPrevSld ) -gBtnArr["nb_next"]= new ImgBtn( "nb_next","nb_nextBorder",30,parent.GoToNextSld ) -gBtnArr["nb_sldshw"]= new ImgBtn( "nb_sldshw","nb_sldshwBorder",18,parent.FullScreen ) -gBtnArr["nb_voice"] = new ImgBtn( "nb_voice","nb_voiceBorder",18,parent.ToggleVNarration ) -gBtnArr["nb_otlTxt"]= new ImgBtn( "nb_otlTxt","nb_otlTxtBorder",23,parent.ToggleOtlText ) -gBtnArr["nb_nts"].m_flagId= "notes_flag" -gBtnArr["nb_nts"].SetFlag = NtsBtnSetFlag -gBtnArr["nb_otlTxt"].ChangeIcon= GetOtlTxtState -var sNext="Next",sPrev="Previous",sEnd="End Show",sFont="Arial", alwaysOn = false -function ShowMenu() -{ - BuildMenu(); - var doc=PPTSld.document.body,x=PPTSld.event.clientX+doc.scrollLeft,y=PPTSld.event.clientY+doc.scrollTop - - m = PPTSld.document.all.item("ctxtmenu") - m.style.pixelLeft=x - if( (x+m.scrollWidth > doc.clientWidth)&&(x-m.scrollWidth > 0) ) - m.style.pixelLeft=x-m.scrollWidth - - m.style.pixelTop=y - if( (y+m.scrollHeight > doc.clientHeight)&&(y-m.scrollHeight > 0) ) - m.style.pixelTop=y-m.scrollHeight - - m.style.display="" -} -function _CM() -{ - if( !parent.IsFullScrMode() && !alwaysOn) return; - - if(!PPTSld.event.ctrlKey) { - ShowMenu() - return false - } else - HideMenu() -} - -function processNavKPH(event) { - if ( PPTSld && (event.keyCode != 13 || !event.srcElement.href || event.srcElement.href == "" ) ) - return PPTSld._KPH(event); -} -function processNavClick() { - HideMenu(); - return true; -} -function BuildMenu() -{ - if( PPTSld.document.all.item("ctxtmenu") ) return - - var mObj=CreateItem( PPTSld.document.body ) -mObj.id="ctxtmenu" - var s=mObj.style - s.position="absolute" - s.cursor="default" - s.width="100px" - SetCMBorder(mObj,"menu","black") - - var iObj=CreateItem( mObj ) - SetCMBorder( iObj, "threedhighlight","threedshadow" ) - iObj.style.padding=2 - if ( self.IsFullScrMode() ) { - CreateMenuItem( iObj,sNext,M_GoNextSld,M_True ) - CreateMenuItem( iObj,sPrev,M_GoPrevSld,M_HasPrevSld ) - } - else { - CreateMenuItem( iObj,sNext, base.TP_GoToNextSld, base.HasNextSld ) - CreateMenuItem( iObj,sPrev,base.GoToPrevSld, base.HasPrevSld ) - } - var sObj=CreateItem( iObj ) - SetCMBorder(sObj,"menu","menu") - var s=sObj.style - s.borderTopColor="threedshadow" - s.borderBottomColor="threedhighlight" - s.height=1 - s.fontSize="0px" - if ( self.IsFullScrMode() ) - CreateMenuItem( iObj,sEnd,M_End,M_True ) - else - CreateMenuItem( iObj,sEnd,M_End,M_False ) -} -function Highlight() { ChangeClr("activecaption","threedhighlight") } -function Deselect() { ChangeClr("threedface","menutext") } -function Perform() -{ - e=PPTSld.event.srcElement - if( e.type=="menuitem" && e.IsActive() ) - e.Action() - else - PPTSld.event.cancelBubble=true -} -function ChangeClr( bg,clr ) -{ - e=PPTSld.event.srcElement - if( e.type=="menuitem" && e.IsActive() ) { - e.style.backgroundColor=bg - e.style.color=clr - } -} - -function M_HasPrevSld() { return( base.HasPrevSld() ) } -function M_GoNextSld() { - base.SetFSMode(1); - if( gIsEndShow ) - M_End(); - else { - if ( base.HasNextSld() ) - base.GoToNextSld(); - else if ( base.EndSlideShow ) { - StartEndShow(); - gIsEndShow = 1; - - PPTNav.location.reload(); - } - else - base.CloseFullScreen(); - } -} -function M_GoPrevSld() { - base.SetFSMode(1); - g_hideNav = 0; - if( gIsEndShow ) { - gIsEndShow = 0; - if ( base.msie > 0 && IsMac() ) - ChangeFrame( SLIDE_FRAME, GetHrefObj( g_currentSlide ).m_slideHref ); - else - PPTSld.history.back(); - - PPTNav.location.reload(); - if( PPTSld.event ) - PPTSld.event.cancelBubble=true; - } - else - base.GoToPrevSld(); -} -function M_True() { return true } -function M_False() { return false } - -function M_End() { - base.CloseFullScreen(); - /*PPTSld.event.cancelBubble=true; - window.close( self )*/ -} - -function CreateMenuItem( node,text,action,eval ) -{ - var e=CreateItem( node ) - e.type="menuitem" - e.Action=action - e.IsActive=eval - e.innerHTML=text - - if( !e.IsActive() ) - e.style.color="threedshadow" - e.onclick=Perform - e.onmouseover=Highlight - e.onmouseout=Deselect - s=e.style; - s.fontFamily=sFont - s.fontSize="8pt" - s.paddingLeft=2 -} -function CreateItem( node ) -{ - var elem=PPTSld.document.createElement("DIV") - node.insertBefore( elem ) - return elem -} -function SetCMBorder( o,ltClr,rbClr ) -{ - var s=o.style - s.backgroundColor="menu" - s.borderStyle="solid" - s.borderWidth=1 - s.borderColor=ltClr+" "+rbClr+" "+rbClr+" "+ltClr -} - -/* netscape context menu */ -g_ctxmenu = 0; -function setRect( obj, X, Y, W, H ) { - obj.top = Y; - obj.left = X; - obj.clip.top = 0; - obj.clip.left = 0; - obj.clip.bottom = H; - obj.clip.right = W; -} - -function KPH(event) { - if ( ! base.IsFullScrMode() && !alwaysOn ) - return true; - - if ( (!IsMac() &&event.which == 3) || ( IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { - PPTSld.g_ctxmenu = 1; - PPTSld.stripUobj.visibility = "show"; - PPTSld.stripDobj.visibility = "show"; - PPTSld.shadeUobj.visibility = "show"; - PPTSld.shadeDobj.visibility = "show"; - PPTSld.panelobj.visibility = "show"; - PPTSld.Fobj.visibility = "show"; - PPTSld.Bobj.visibility = "show"; - PPTSld.Eobj.visibility = "show"; - - setRect(PPTSld.shadeUobj, event.pageX-2, event.pageY-2, 82, 67 ); - setRect(PPTSld.shadeDobj, event.pageX, event.pageY, 82, 67 ); - setRect(PPTSld.panelobj, event.pageX, event.pageY, 80, 65 ); - setRect(PPTSld.Fobj, event.pageX, event.pageY, 80, 20 ); - setRect(PPTSld.Bobj, event.pageX, event.pageY+20, 80, 20 ); - setRect(PPTSld.stripUobj, event.pageX, event.pageY+41, 80, 1 ); - setRect(PPTSld.stripDobj, event.pageX, event.pageY+43, 80, 1 ); - setRect(PPTSld.Eobj, event.pageX, event.pageY+45, 80, 20 ); - return false; - } - if ( HitOK( event ) ) { - PPTSld.g_ctxmenu = 0; - PPTSld.stripUobj.visibility = "hide"; - PPTSld.stripDobj.visibility = "hide"; - PPTSld.shadeUobj.visibility = "hide"; - PPTSld.shadeDobj.visibility = "hide"; - PPTSld.panelobj.visibility = "hide"; - PPTSld.Fobj.visibility = "hide"; - PPTSld.Bobj.visibility = "hide"; - PPTSld.Eobj.visibility = "hide"; - } - return true; -} - -function overMe() { - this.bgColor = "blue"; -} - -function outMe() { - this.bgColor = "#AAAAAA"; -} - -function makeElement( whichEl, whichContainer ) { - if ( arguments.length == 1 ) { - whichContainer = PPTSld; - } - tmp = new Layer(100,whichContainer); - eval( whichEl + " = tmp" ); - return eval(whichEl); -} - -function initMe( obj, clr, text ) { - obj.bgColor = clr; -// obj.document.write("<a href='javascript:return false'>" + text + "</a>"); - obj.document.write( "<font size=2 face=Arial " ); - if ( !M_HasPrevSld() && (obj == PPTSld.Bobj ) ) { - obj.document.write( " color='#808080' " ); - } - else { - obj.onmouseover = overMe; - obj.onmouseout = outMe; - } - obj.document.write( " >   " + text +"</font> <layer top=0 left=0 width=100 height=40 ></layer>"); - obj.document.close(); - obj.captureEvents(Event.CLICK); - obj.color = "black"; -} - -function createCM() { - if ( base.IsFullScrMode() ) { - var clr = "#AAAAAA"; - PPTSld.shadeUobj = makeElement("SHADEU"); - PPTSld.shadeDobj = makeElement("SHADED"); - PPTSld.panelobj = makeElement("PANEL"); - PPTSld.stripUobj = makeElement("STRIPU"); - PPTSld.stripDobj = makeElement("STRIPD"); - PPTSld.shadeUobj.bgColor = "#BBBBBB"; - PPTSld.shadeDobj.bgColor = "#888888"; - PPTSld.stripUobj.bgColor = "#777777"; - PPTSld.stripDobj.bgColor = "#CCCCCC"; - PPTSld.panelobj.bgColor = clr; - PPTSld.Fobj = makeElement("Next"); - PPTSld.Bobj = makeElement("Previous"); - PPTSld.Eobj = makeElement("EndShow"); - initMe( PPTSld.Fobj, clr, "Next" ); - PPTSld.Fobj.onclick = M_GoNextSld; - - initMe( PPTSld.Bobj, clr, "Previous" ); - PPTSld.Bobj.onclick = M_GoPrevSld; - - initMe( PPTSld.Eobj, clr, "End Show"); - PPTSld.Eobj.onclick = base.CloseFullScreen; - } -} - -function IsContextMenu() { - return (g_ctxmenu == 1) -} -var g_notesTable = new Array()
-var g_hiddenSlide = new Array()
-makeSlide( 0,1,1);
-makeSlide( 1,1,1);
-makeSlide( 2,1,1);
-makeSlide( 3,1,1);
-makeSlide( 4,1,1);
-makeSlide( 5,1,1);
-makeSlide( 6,1,1);
-makeSlide( 7,1,1);
-makeSlide( 8,1,1);
-makeSlide( 9,1,1);
-makeSlide( 10,1,1);
-makeSlide( 11,1,1);
-makeSlide( 12,1,1);
-makeSlide( 13,1,1);
-makeSlide( 14,1,1);
-makeSlide( 15,1,1);
-makeSlide( 16,1,1);
-makeSlide( 17,1,1);
-makeSlide( 18,1,1);
-makeSlide( 19,1,1);
-makeSlide( 20,1,1);
-makeSlide( 21,1,1);
-makeSlide( 22,1,1);
-makeSlide( 23,1,1);
-makeSlide( 24,1,1);
-makeSlide( 25,1,1);
-makeSlide( 26,1,1);
-makeSlide( 27,1,1);
-makeSlide( 28,1,1);
-makeSlide( 29,1,1);
-makeSlide( 30,1,1);
-makeSlide( 31,1,1);
- -var END_SHOW_HREF = "endshow.htm", - OUTLINE_EXPAND_HREF = "outline_expanded.htm", - OUTLINE_COLLAPSE_HREF = "outline_collapsed.htm", - OUTLINE_NAVBAR_HREF = "outline_navigation_bar.htm", - NAVBAR_HREF = "navigation_bar.htm", - BLANK_NOTES_HREF = "blank_notes.htm", - NUM_VISIBLE_SLIDES = 32, - SIMPLE_FRAMESET = 0, - SLIDE_FRAME = "PPTSld", - NOTES_FRAME = "PPTNts", - OUTLINE_FRAME = "PPTOtl", - OUTLINE_NAVBAR_FRAME = "PPTOtlNav", - NAVBAR_FRAME = "PPTNav", - MAIN_FRAME = "MainFrame", - FS_NAVBAR_HREF = "fs_navigation_bar.htm", - isIEFiles = 2, - isNAVFiles = 8, - isFLATFiles = 16, - includeNotes = 1, - PPTPRESENTATION = 1; -var INITSLIDENUM = 1; - -var EndSlideShow = 0; -var g_outline_href = OUTLINE_COLLAPSE_HREF; -var g_fullscrMode = 0; -var FSWin = null; -var gtmpstr = document.location.href; -var g_baseURL = gtmpstr.substr(0, gtmpstr.lastIndexOf("/") ) + "/" + "WebQTLDemo_files"; -var g_showoutline = 1; -var g_shownotes = includeNotes; -var g_currentSlide = INITSLIDENUM, g_prevSlide = INITSLIDENUM; -var saveFSSlideNum = saveTPSlideNum = g_currentSlide; -var saveFSprevSlide = saveTPprevSlide = g_prevSlide; -var g_slideType="ie"; -var appVer = navigator.appVersion; -var msie = appVer.indexOf( "MSIE " ) + appVer.indexOf( "Internet Explorer " ); -var isnav = ( navigator.appName.indexOf( "Netscape" ) >= 0 ); -var msieWin31 = (appVer.indexOf( "Windows 3.1" ) > 0); -var ver = 0; -var g_done = 0; -var g_prevotlobjidx = 0; -var g_ShowFSDefault = 0; -var g_lastVisibleSld = 1; -var g_allHidden = false; -function IsIE() { - return (msie >= 0 ); -} - -function IsNav() { - return (isnav); -} -var msiePos = appVer.indexOf( "MSIE " ); -var inexPos = appVer.indexOf( "Internet Explorer " ); -if ( msiePos >= 0 ) - ver = parseFloat( appVer.substring( msiePos+5, appVer.indexOf ( ";", msiePos ) ) ); -else if( inexPos >= 0 ) - ver=parseFloat( appVer.substring( inexPos+18, appVer.indexOf(";",inexPos) ) ) -else - ver = parseInt( appVer ); - -//var g_supportsPPTHTML = 0; //!msieWin31 && ( ( msie >= 0 && ver >= 3.02 ) || ( msie < 0 && ver >= 3 ) ); - -function GetCurrentSlideNum() -{ - obj = GetHrefObj( g_currentSlide ); - if ( GetHrefObj( g_currentSlide ).m_origVisibility == 1 ) - return obj.m_slideIdx; - else - return g_currentSlide; -} - -function GetNumSlides() -{ - if ( GetHrefObj( g_currentSlide ).m_origVisibility == 1 ) - return NUM_VISIBLE_SLIDES; - else - return g_docTable.length; -} - -function GetHrefObj( slideIdx ) -{ return g_docTable[slideIdx - 1]; -} - -function GetSlideNum( slideHref ) -{ - for (ii=0; ii<g_docTable.length; ii++) { - if ( g_docTable[ii].m_slideHref == slideHref ) - return ii+1; - } - return 1; -} - -function GoToNextSld() -{ - targetIdx = g_currentSlide + 1; - if ( GetHrefObj( targetIdx-1 ).m_origVisibility == 0 ) { - if ( targetIdx<=g_docTable.length ) { - obj = GetHrefObj( targetIdx ); - obj.m_visibility = 1; - GoToSld( obj.m_slideHref ); - } - } - else { - obj = GetHrefObj( targetIdx ); - while ( obj && ( obj.m_origVisibility == 0 ) && ( targetIdx<=g_docTable.length ) ) - obj = GetHrefObj( targetIdx++ ); - if( obj && obj.m_origVisibility ) - GoToSld( obj.m_slideHref ); - } -} - -function GoToPrevSld() -{ - targetIdx = g_currentSlide - 1; - if ( targetIdx > 0 ) { - obj = GetHrefObj( targetIdx ); - while ( ( obj.m_visibility == 0 ) && ( targetIdx>0 ) ) - obj = GetHrefObj( targetIdx-- ); - GoToSld( obj.m_slideHref ); - } -} - -function GoToLast() -{ - targetIdx = g_docTable.length; - if ( targetIdx != g_currentSlide ) - GoToSld( GetHrefObj( targetIdx ).m_slideHref ); -} - -function GoToFirst() -{ GoToSld( GetHrefObj(1).m_slideHref ); -} - -function highlite() { - if ( IsFullScrMode() ) - return; - index = GetCurrentSlideNum(); - if ( !frames[MAIN_FRAME].frames[OUTLINE_FRAME] ) - return; - if ( msie < 0 ) { - if ( g_prevotlobjidx != 0 ) { - eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.LAYERID" + g_prevotlobjidx ); - otlobj.hidden = true; - } - else - index = GetCurrentSlideNum(); - eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.LAYERID" + index ); - otlobj.hidden = false; - - g_prevotlobjidx = index; - - return; - } - if ( !g_showoutline ) - return; - - backclr = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.body.bgColor; - textclr = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.body.text; - if ( g_prevotlobjidx != 0 ) { - eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.all.p" + g_prevotlobjidx ); - otlobj.style.backgroundColor = backclr; - otlobj.style.color = textclr; - otlobj.all.AREF.style.color = textclr; - } - else - index = GetCurrentSlideNum(); - eval( "otlobj = frames[MAIN_FRAME].frames[OUTLINE_FRAME].document.all.p" + index ); - otlobj.style.backgroundColor = textclr; - otlobj.style.color = backclr; - otlobj.all.AREF.style.color = backclr; - g_prevotlobjidx = index; -} - -function ChangeFrame( frame, href ) -{ -if ( IsFramesMode() ) { - if ( NAVBAR_FRAME == frame || OUTLINE_NAVBAR_FRAME == frame ) { - frames[frame].location.replace(href); - } - else if( ! ( ( OUTLINE_FRAME == frame && !g_showoutline) || (NOTES_FRAME == frame && !g_shownotes ) ) ){ - frames[MAIN_FRAME].frames[frame].location.href = href; - } - } - else { - if ( frame == NAVBAR_FRAME || frame == SLIDE_FRAME ) { - if( frame == NAVBAR_FRAME ) { - href = FS_NAVBAR_HREF; - - } - if( frame == NAVBAR_FRAME ) - window.frames[frame].location.replace(href); - else - window.frames[frame].location.href = href; - } - } - -} - -function shutEventPropagation() { - if ( IsNav() ) - return; - - var slideFrame; - if ( IsFramesMode() ) - slideFrame = frames[MAIN_FRAME].frames[SLIDE_FRAME]; - else - slideFrame = window.frames[SLIDE_FRAME]; - if ( slideFrame.event ) - slideFrame.event.cancelBubble=true; -} - -function GoToSld( slideHref ) -{ - shutEventPropagation(); - if ( slideHref != GetHrefObj( g_currentSlide ).m_slideHref || g_slideType != GetHrefObj( g_currentSlide ).type) { - g_prevSlide = g_currentSlide; - g_currentSlide = GetSlideNum( slideHref ); - g_slideType = GetHrefObj( g_currentSlide ).type; - obj = GetHrefObj( g_currentSlide ); - obj.m_visibility = 1; - ChangeFrame( SLIDE_FRAME, slideHref ); - if( !SIMPLE_FRAMESET ) - ChangeFrame( NOTES_FRAME, obj.m_notesHref ); - ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF ); - - } -} - -function PrevSldViewed() -{ GoToSld( GetHrefObj( g_prevSlide ).m_slideHref ); -} - -function NoHref() {} - -function ExpandOutline( ) -{ - g_outline_href = OUTLINE_EXPAND_HREF; - ChangeFrame( OUTLINE_FRAME, OUTLINE_EXPAND_HREF ); - frames[OUTLINE_NAVBAR_FRAME].location.replace( OUTLINE_NAVBAR_HREF); -} - -function CollapseOutline() -{ - g_outline_href = OUTLINE_COLLAPSE_HREF; - ChangeFrame( OUTLINE_FRAME, OUTLINE_COLLAPSE_HREF ); - frames[OUTLINE_NAVBAR_FRAME].location.replace( OUTLINE_NAVBAR_HREF); - } - -function SlideUpdated( id ) -{ - if ( id != GetHrefObj( g_currentSlide ).m_slideHref ) { - g_prevSlide = g_currentSlide; - g_currentSlide = GetSlideNum( id ); - obj = GetHrefObj( g_currentSlide ); - if( !SIMPLE_FRAMESET ) - ChangeFrame( NOTES_FRAME, obj.m_notesHref ); 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<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description
content="Jun-19-03: WebQTL Demonstration One please link to www.webqtl.org/search.html">
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</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:6.89%;left:3.31%;width:96.42%;height:19.61%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232;
mso-text-indent-alt:0;position:absolute;top:0%;left:1.09%;width:97.39%;
height:100.0%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-size:68%'><i>WebQTL Demonstration One<br>
</i></span></span><span
style='position:absolute;top:33.33%;left:4.23%;width:95.76%'><span
style='font-size:68%'><i>please link to <br>
</i></span></span><span
style='position:absolute;top:58.55%;left:4.23%;width:95.76%'><span
style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span
style='font-size:68%;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
</div>
<div style='position:absolute;top:31.62%;left:5.43%;width:73.24%;height:45.05%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='position:absolute;top:0%;left:2.71%;width:97.28%;
height:93.33%'>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:0%;width:89.77%;height:39.91%'><span
style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format:
nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:
99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part
1: How to discover shared </span></span><span style='position:absolute;
top:30.52%;left:7.86%;width:86.54%'><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>expression patterns (slides </span></span><span
style='position:absolute;top:61.05%;left:7.86%;width:86.54%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'>2Ð14)<br>
</span></span></div>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:48.31%;left:0%;width:84.94%;height:27.73%'><span
style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format:
nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:
99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part
2. Discovering upstream </span></span><span style='position:absolute;
top:43.93%;left:8.31%;width:91.46%'><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>modulators (15Ð25)<br>
</span></span></div>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:84.45%;left:0%;width:100.0%;height:15.54%'><span
style='position:absolute;top:0%;left:7.06%;width:92.93%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:
"numbullet3\,3";color:#FBFDB8;position:absolute;left:-7.6%;font-family:Times;
font-size:99%'>3.</span></span><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>Discovering downstream targets</span></span></div>
</div>
</div>
<img border=0 src="slide0001_image001.gif" style='position:absolute;top:21.9%;
left:74.56%;width:23.57%;height:64.31%'>
<div class=O style='position:absolute;top:79.32%;left:75.89%;width:10.46%;
height:14.48%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:42.68%'><span
style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span
style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E;
display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:46.34%;left:0%;width:82.27%;height:54.87%'><span
style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<div class=O style='position:absolute;top:76.5%;left:4.37%;width:78.67%;
height:13.07%'><span style='position:absolute;top:0%;left:0%;width:98.98%'><span
style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index:
3'><i>PowerPoint ÒNormal viewÓ has notes that </i></span></span><span
style='position:absolute;top:51.35%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index:
3'><i>may be useful companions to these slides.</i></span><span
style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index:
3;mso-special-format:lastCR;display:none'><br>
</span></span></div>
</div>
<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=Helvetica size=3>Welcome to a short
demonstation of WebQTL. Please adjust the wize of windows on your monitor so
that you can see part of this page as well as WebQTL windows. WebQTL will
produce a potentially large number of new windows (pop-ups), so you may need
to modify your browser preferences to permit pop-ups.<span
style="mso-spacerun: yes"> </span>In this demonstration, we
explore one important transcript expressed in the brain: the amyloid beta
precursor protein messenger RNA. The product of this mRNA, the APP protein,
is associated with Alzheimer disease.</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=Helvetica size=3>(Initial version of June
2003 by Rob Williams, Last edits June 16, 2003 by RW.)</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0001_image001.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0001_image001.gif Binary files differdeleted file mode 100755 index 5bcd338f..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0001_image001.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm deleted file mode 100755 index 0df634c1..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>Welcome to a short
demonstation of WebQTL. Please adjust the wize of windows on your monitor so
that you can see part of this page as well as WebQTL windows. WebQTL will
produce a potentially large number of new windows (pop-ups), so you may need
to modify your browser preferences to permit pop-ups.<span
style="mso-spacerun: yes"> </span>In this demonstration, we
explore one important transcript expressed in the brain: the amyloid beta
precursor protein messenger RNA. The product of this mRNA, the APP protein,
is associated with Alzheimer disease.</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=Helvetica size=2>(Initial version of June
2003 by Rob Williams, Last edits June 16, 2003 by RW.)</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0002.htm deleted file mode 100755 index 2efd97f9..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0002.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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width:6.0in !important;
height:4.5in !important;
font-size:76% !important;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--
-gId="slide0002.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
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</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:6.89%;left:2.78%;width:93.77%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:2.11%;width:96.46%;height:50.6%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>or webqtl.org/search.html (mirror)</span></div>
</div>
<img border=0 src="slide0002_image002.gif" style='position:absolute;top:16.6%;
left:2.51%;width:71.65%;height:81.27%'><img border=0
src="slide0002_image003.gif" style='position:absolute;top:49.82%;left:42.38%;
width:20.39%;height:7.59%'><img border=0 src="slide0002_image004.gif"
style='position:absolute;top:50.35%;left:62.78%;width:15.09%;height:36.74%'>
<div class=O style='position:absolute;top:60.42%;left:79.33%;width:15.76%;
height:11.48%'>
<div style='position:absolute;top:0%;left:0%;width:100.0%;height:49.23%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>choose a<br>
</span></div>
<div style='position:absolute;top:50.76%;left:0%;width:96.63%;height:49.23%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>database</span></div>
</div>
<div class=O style='position:absolute;top:46.46%;left:79.33%;width:21.05%;
height:11.48%'>
<div style='position:absolute;top:0%;left:0%;width:89.93%;height:49.23%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>enter<br>
</span></div>
<div style='position:absolute;top:50.76%;left:0%;width:100.0%;height:49.23%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'><i>amyloid beta</i></span><span style='font-family:"Gill Sans";font-size:
250%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</div>
<div class=O style='position:absolute;top:78.26%;left:79.73%;width:11.52%;
height:11.48%'>
<div style='position:absolute;top:0%;left:0%;width:89.65%;height:49.23%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>select<br>
</span></div>
<div style='position:absolute;top:50.76%;left:0%;width:100.0%;height:49.23%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>search</span></div>
</div>
<div style='position:absolute;top:.88%;left:3.31%;width:93.77%;height:9.36%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div style='position:absolute;top:0%;left:1.12%;width:97.45%;height:79.24%'>
<div class=B1 style='mso-margin-left-alt:644;mso-text-indent-alt:420'></div>
<div class=B2 style='mso-margin-left-alt:937;mso-text-indent-alt:716'></div>
<div class=B3 style='mso-margin-left-alt:1232;mso-text-indent-alt:1009'></div>
<div class=B4 style='mso-margin-left-alt:1544;mso-text-indent-alt:1304'></div>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
0;position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>link to www.webqtl.org/search.html</span></div>
</div>
</div>
</div>
<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=Helvetica size=3>WebQTL can be used to
enter your own trait data or to work with data that we have entered for you.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Linking to
http://www.webqtl.org/search.html will get you a version of the window above.
It may not be identical in layout but it will have the key features. Please
follow the intructions on the slide. Of course, we encourage you to enter
your own terms of interest.</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=Helvetica size=3>Two points: If you make
a search term too complex you may get no hits. if you make it too simple (for
example, APP) then you may get too much. Experiment.</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=Helvetica size=3>If you just link to</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>http://www.webqtl.org
you will NOT see the window above but will see text that will help you to
enter your own data.<span style="mso-spacerun: yes"> </span>To get to a
version of the window shown above you will need to click on the phrase<span
style="mso-spacerun: yes"> </span>RNA expression and Phenotype
Databases in the upper banner.</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=Helvetica size=3>If you do not get a new
page within 30 seconds then there is<span style="mso-spacerun: yes">
</span>a problem: try the mirror site http://webqtl.org/search.html.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image002.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image002.gif Binary files differdeleted file mode 100755 index 304daa18..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image002.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image003.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image003.gif Binary files differdeleted file mode 100755 index 74f73adc..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image003.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image004.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0002_image004.gif Binary files differdeleted file mode 100755 index 1da7043d..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0002_image004.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm deleted file mode 100755 index 266bf3fb..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>WebQTL can be used to
enter your own trait data or to work with data that we have entered for you.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Linking to
http://www.webqtl.org/search.html will get you a version of the window above.
It may not be identical in layout but it will have the key features. Please
follow the intructions on the slide. Of course, we encourage you to enter
your own terms of interest.</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=Helvetica size=2>Two points: If you make
a search term too complex you may get no hits. if you make it too simple (for
example, APP) then you may get too much. Experiment.</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=Helvetica size=2>If you just link to</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>http://www.webqtl.org
you will NOT see the window above but will see text that will help you to
enter your own data.<span style="mso-spacerun: yes"> </span>To get to a
version of the window shown above you will need to click on the phrase<span
style="mso-spacerun: yes"> </span>RNA expression and Phenotype
Databases in the upper banner.</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=Helvetica size=2>If you do not get a new
page within 30 seconds then there is<span style="mso-spacerun: yes">
</span>a problem: try the mirror site http://webqtl.org/search.html.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0003.htm deleted file mode 100755 index 7e0f4be9..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0003.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content="Jun-19-03: Search results">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
<!--.sld
{left:0px !important;
width:6.0in !important;
height:4.5in !important;
font-size:76% !important;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--
-gId="slide0003.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img
border=0 src="slide0003_image005.gif" style='position:absolute;top:9.36%;
left:9.13%;width:59.73%;height:87.45%'><img border=0
src="slide0003_image006.gif" style='position:absolute;top:72.26%;left:14.03%;
width:62.51%;height:6.53%'>
<div class=O style='position:absolute;top:68.37%;left:78.54%;width:21.05%;
height:17.31%'>
<div style='position:absolute;top:0%;left:0%;width:89.93%;height:32.65%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>highlight<br>
</span></div>
<div style='position:absolute;top:33.67%;left:0%;width:100.0%;height:32.65%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'><i>amyloid beta<br>
</i></span></div>
<div style='position:absolute;top:67.34%;left:0%;width:89.93%;height:32.65%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>then click</span><span style='font-family:"Gill Sans";font-size:250%;
color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:-4.59%;left:7.81%;width:84.9%;height:18.55%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='position:absolute;top:24.76%;left:1.56%;width:96.87%;
height:46.66%'><span style='font-size:91%'>Search results</span><span
style='mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<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=Helvetica size=3>If all goes well, you
will see a version of this window. WebQTL will display up to about 100 hits.
If a search generates larger numbers of hits then you will need to refine
your search terms.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image005.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image005.gif Binary files differdeleted file mode 100755 index 5c7d29e8..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image005.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif Binary files differdeleted file mode 100755 index f75379b9..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm deleted file mode 100755 index 5dbbbd2e..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>If all goes well, you
will see a version of this window. WebQTL will display up to about 100 hits.
If a search generates larger numbers of hits then you will need to refine
your search terms.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0004.htm deleted file mode 100755 index 9980cf8b..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0004.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<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><script language=JavaScript><!--
-gId="slide0004.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.41%;left:1.72%;width:97.61%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:2.03%;width:97.96%;height:50.6%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>First page of data: The ÒTrait Data FormÓ</span></div>
</div>
<img border=0 src="slide0004_image007.gif" style='position:absolute;top:11.13%;
left:3.31%;width:77.61%;height:86.39%'><img border=0
src="slide0004_image008.gif" style='position:absolute;top:56.0%;left:66.88%;
width:14.7%;height:7.42%'>
<div class=O style='position:absolute;top:50.7%;left:81.85%;width:20.0%;
height:27.2%'>
<div style='position:absolute;top:0%;left:0%;width:100.0%;height:20.12%'><span
style='font-size:200%;color:#E9EB5D'><i>Click here<br>
</i></span></div>
<div style='position:absolute;top:19.48%;left:0%;width:83.44%;height:20.12%'><span
style='font-size:200%;color:#E9EB5D'><i>to learn<br>
</i></span></div>
<div style='position:absolute;top:39.61%;left:0%;width:83.44%;height:20.12%'><span
style='font-size:200%;color:#E9EB5D'><i>about<br>
</i></span></div>
<div style='position:absolute;top:59.09%;left:0%;width:83.44%;height:20.12%'><span
style='font-size:200%;color:#E9EB5D'><i>data<br>
</i></span></div>
<div style='position:absolute;top:79.22%;left:0%;width:83.44%;height:20.12%'><span
style='font-size:200%;color:#E9EB5D'><i>source</i></span></div>
</div>
</div>
<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=Helvetica size=3>The Trait Data and
Editing Form is the single more important page from the point of view of
working with WebQTL data. Please read the text carefully. Explore the links,
but do not close this page. We will need it many more times in this
demonstration.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>The Trait Data and
Editing Form is the single more important page from the point of view of
working with WebQTL data. Please read the text carefully. Explore the links,
but do not close this page. We will need it many more times in this
demonstration.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0005.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0005.htm deleted file mode 100755 index ab904a72..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0005.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<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><script language=JavaScript><!--
-gId="slide0005.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.41%;left:3.31%;width:96.29%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:2.06%;width:97.93%;height:50.6%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>Data sources: Phenotpyes and genotypes</span></div>
</div>
<img border=0 src="slide0005_image009.gif" style='position:absolute;top:10.77%;
left:7.68%;width:84.5%;height:88.33%'></div>
<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=Helvetica size=3>There are already five
databases in WebQTL. Each will eventually have a page like this describing
the data source and appropriate citations to these databases. The great
majority of data in WebQTL were generated in our own labs and those of our
collaborators.<span style="mso-spacerun: yes"> </span>We welcome you to
use these data, but caution you that there are inevitably lots of little
problems and issues that may compromise some results. Be cautious and
skeptical. Ask us questions before you leap to publication. And please, if
you find the data useful or can verify or refute data, LET US KNOW. We would
like to add you to our reference section and add links to improvements.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif Binary files differdeleted file mode 100755 index a6596e12..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm deleted file mode 100755 index 916084ec..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>There are already five
databases in WebQTL. Each will eventually have a page like this describing
the data source and appropriate citations to these databases. The great
majority of data in WebQTL were generated in our own labs and those of our
collaborators.<span style="mso-spacerun: yes"> </span>We welcome you to
use these data, but caution you that there are inevitably lots of little
problems and issues that may compromise some results. Be cautious and
skeptical. Ask us questions before you leap to publication. And please, if
you find the data useful or can verify or refute data, LET US KNOW. We would
like to add you to our reference section and add links to improvements.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0006.htm deleted file mode 100755 index f3d4d1d5..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0006.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<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><script language=JavaScript><!--
-gId="slide0006.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.06%;left:1.72%;width:47.94%;height:7.24%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:4.87%;left:4.14%;width:95.85%;height:78.04%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:81%;color:#E9EB5D;mso-color-index:
3'>Return to Trait Data page </span></div>
</div>
<img border=0 src="slide0006_image010.gif" style='position:absolute;top:7.77%;
left:.79%;width:48.47%;height:79.32%'><img border=0 src="slide0006_image011.gif"
style='position:absolute;top:7.77%;left:50.46%;width:48.6%;height:78.79%'>
<div style='position:absolute;top:1.06%;left:52.45%;width:43.84%;height:13.78%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:2.56%;left:4.53%;width:92.44%;height:41.02%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:81%;color:#E9EB5D;mso-color-index:
3'>bottom of this page</span></div>
</div>
<div class=O style='position:absolute;top:86.39%;left:3.44%;width:109.13%;
height:11.48%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>Trait data for each strain with SE when known. For array data </span></span><span
style='position:absolute;top:50.76%;left:0%;width:99.02%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>the scale is ~ log base 2.<span style="mso-spacerun: yes">
</span></span><span style='font-size:183%;color:#E9EB5D;mso-color-index:3'>F1=13.752
= 2^13.752 = 13796 </span><span style='font-family:"Gill Sans";font-size:183%;
color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;display:none'><br>
</span></span></div>
</div>
<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=Helvetica size=3>This<span
style="mso-spacerun: yes"> </span>slide shows you the<span
style="mso-spacerun: yes"> </span>lower parts of the Trait Data Page.
We expect to make many small modification of this page, so do not be
surprised if some elements have been moved around.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif Binary files differdeleted file mode 100755 index 967e59ca..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif Binary files differdeleted file mode 100755 index 1e1432cf..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm deleted file mode 100755 index be43575c..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>This<span
style="mso-spacerun: yes"> </span>slide shows you the<span
style="mso-spacerun: yes"> </span>lower parts of the Trait Data Page.
We expect to make many small modification of this page, so do not be
surprised if some elements have been moved around.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0007.htm deleted file mode 100755 index 052d2dcf..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0007.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<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><script language=JavaScript><!--
-gId="slide0007.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.41%;left:3.31%;width:93.77%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:2.11%;width:97.45%;height:50.6%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>Discovering shared expression patterns</span></div>
</div>
<img border=0 src="slide0007_image012.gif" style='position:absolute;top:16.6%;
left:5.03%;width:86.22%;height:55.47%'><img border=0
src="slide0007_image013.gif" style='position:absolute;top:60.42%;left:45.82%;
width:13.77%;height:14.84%'></div>
<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=Helvetica size=3>Finally, we can now
start an analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>We ask a simple
question:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Do differences in App
transcript expression correlate with those of any other transcripts in the
forebrain?</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007_image012.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0007_image012.gif Binary files differdeleted file mode 100755 index 9cde2f15..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0007_image012.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007_image013.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0007_image013.gif Binary files differdeleted file mode 100755 index df9c9efb..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0007_image013.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm deleted file mode 100755 index 7d2536da..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>Finally, we can now
start an analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>We ask a simple
question:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Do differences in App
transcript expression correlate with those of any other transcripts in the
forebrain?</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0008.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0008.htm deleted file mode 100755 index 7b1d488d..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0008.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<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><script language=JavaScript><!--
-gId="slide0008.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.41%;left:3.31%;width:93.77%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:2.11%;width:96.46%;height:50.6%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>The </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript neighborhood</span></div>
</div>
<img border=0 src="slide0008_image014.gif" style='position:absolute;top:10.77%;
left:5.82%;width:66.62%;height:88.33%'>
<div class=O style='position:absolute;top:30.74%;left:75.23%;width:26.22%;
height:18.72%'><span style='position:absolute;top:0%;left:0%;width:91.91%'><span
style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>Question: </b></span><span
style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>How </b></span></span><span
style='position:absolute;top:21.69%;left:0%;width:97.47%'><span
style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>many transcripts </b></span></span><span
style='position:absolute;top:40.56%;left:0%;width:100.0%'><span
style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>have correlations </b></span></span><span
style='position:absolute;top:59.43%;left:0%;width:97.97%'><span
style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>>0.7? What does </b></span></span><span
style='position:absolute;top:79.24%;left:0%;width:85.35%'><span
style='font-size:133%;color:#E9EB5D;mso-color-index:3'><b>this imply.</b></span></span></div>
</div>
<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=Helvetica size=3>The answer is a strong
Yes. A very large number of transcripts have correlations above 0.7 (absolute
value) with App mRNA. The precise number today is 208. But this will change
as we add more strains and arrays. In any case, this is a fairly large number
and all of these correlations are significant at alpha .05 even when
correcting for the enormous numbers<span style="mso-spacerun: yes">
</span>of tests (12422 tests).</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=Helvetica size=3>What does this imply?</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=Helvetica size=3>That there can be
massive codependence of expression variance among transcripts. App is NOT an
isolated instance. This is improtant biologically and statistically. From a
statistical perspective, we would like to know how many ÒindependentÓ test we
effectively are performing when we use array data in this way. Are we testing
12000 independent transcripts or just 1200 transcriptional ÒmodulesÓ each
with blurred boarders but each with about 10 effective members. There is no
answer yet, but we probaby have a large enough data set to begin to answer
this question.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0008_image014.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0008_image014.gif Binary files differdeleted file mode 100755 index d555e779..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0008_image014.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm deleted file mode 100755 index 5003f4a6..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>The answer is a strong
Yes. A very large number of transcripts have correlations above 0.7 (absolute
value) with App mRNA. The precise number today is 208. But this will change
as we add more strains and arrays. In any case, this is a fairly large number
and all of these correlations are significant at alpha .05 even when
correcting for the enormous numbers<span style="mso-spacerun: yes">
</span>of tests (12422 tests).</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=Helvetica size=2>What does this imply?</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=Helvetica size=2>That there can be
massive codependence of expression variance among transcripts. App is NOT an
isolated instance. This is improtant biologically and statistically. From a
statistical perspective, we would like to know how many ÒindependentÓ test we
effectively are performing when we use array data in this way. Are we testing
12000 independent transcripts or just 1200 transcriptional ÒmodulesÓ each
with blurred boarders but each with about 10 effective members. There is no
answer yet, but we probaby have a large enough data set to begin to answer
this question.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0009.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0009.htm deleted file mode 100755 index 82b93d4f..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0009.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:2.47%;left:6.62%;width:94.17%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:2.1%;width:98.03%;height:50.6%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>Handdrawn sketch of the neighborhood</span></div>
</div>
<img border=0 src="slide0009_image015.gif" style='position:absolute;top:13.07%;
left:9.53%;width:80.79%;height:80.38%'></div>
<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=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"> </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>
<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=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>
</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=Helvetica size=3>What are all of the<span
style="mso-spacerun: yes"> </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"> </span>ÒatÓ. 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"> </span>If there is no star symbol, then it
is not even formally ÒsuggestiveÓ but does make an interesting looking blip
on the QTL radar screen.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0009_image015.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0009_image015.gif Binary files differdeleted file mode 100755 index 4e9f96be..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0009_image015.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm deleted file mode 100755 index bdcc6cd9..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
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href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>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"> </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>
<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=Helvetica size=2>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>
</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=Helvetica size=2>What are all of the<span
style="mso-spacerun: yes"> </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=2>1.</font><font
face=Helvetica size=2>The official gene symbol = App</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>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=2>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=2>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"> </span>ÒatÓ. 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=2>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=2>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"> </span>If there is no star symbol, then it
is not even formally ÒsuggestiveÓ but does make an interesting looking blip
on the QTL radar screen.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0010.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0010.htm deleted file mode 100755 index 07768218..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0010.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.41%;left:3.31%;width:107.54%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:1.84%;width:98.15%;height:85.54%'><span
style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format:
nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:
99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>What
a network is likely to look like (but </span><span style='font-size:106%;
color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;
color:#E9EB5D;mso-color-index:3'> </span></span><span style='position:absolute;
top:39.43%;left:4.76%;width:80.92%'><span style='font-size:106%;color:#E9EB5D;
mso-color-index:3'>will not be center of universe).</span></span></div>
</div>
<img border=0 src="slide0010_image016.gif" style='position:absolute;top:15.19%;
left:6.35%;width:71.92%;height:82.5%'>
<div class=O style='position:absolute;top:32.86%;left:45.82%;width:5.96%;
height:3.71%'><span style='font-size:133%;color:#FF0F0F'><b><i>App</i></b></span></div>
</div>
<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=Helvetica size=3>What networks are likely
to really look like. This slide is taken from Lumeta Inc.<span
style="mso-spacerun: yes"> </span>(www.lumeta.com). It actually
illustrates the structure of connections across the<span style="mso-spacerun:
yes"> </span>Internet. The large green area is a major Internet
provider (WorldCom before the fall?).<span style="mso-spacerun: yes">
</span>Check<span style="mso-spacerun: yes"> </span>out Lumeta to see
some more lovely graphs of this sort. Most biologists are familiar with
simple sketches, but this is what we will have to be prepared to contend with
soon.</font><br>
</td>
</tr>
</table>
</div>
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<head>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
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<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>What networks are likely
to really look like. This slide is taken from Lumeta Inc.<span
style="mso-spacerun: yes"> </span>(www.lumeta.com). It actually
illustrates the structure of connections across the<span style="mso-spacerun:
yes"> </span>Internet. The large green area is a major Internet
provider (WorldCom before the fall?).<span style="mso-spacerun: yes">
</span>Check<span style="mso-spacerun: yes"> </span>out Lumeta to see
some more lovely graphs of this sort. Most biologists are familiar with
simple sketches, but this is what we will have to be prepared to contend with
soon.</font><br>
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</table>
</body>
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genomics</title>
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width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:3.53%;left:2.11%;width:97.48%;height:21.02%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232;
mso-text-indent-alt:0;position:absolute;top:18.48%;left:.95%;width:99.04%;
height:61.34%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-size:68%'><i>Are there experimental results to corroborate a link </i></span></span><span
style='position:absolute;top:49.31%;left:4.25%;width:90.12%'><span
style='font-size:68%'><i>between App with Hsp84-1?</i></span></span></div>
</div>
<div style='position:absolute;top:82.15%;left:4.1%;width:96.42%;height:18.55%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div>
<div class=O style='position:absolute;top:29.5%;left:4.37%;width:99.33%;
height:13.07%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D'><i>Yes: Heat shock
84-1 induces the expression of App, </i></span></span><span style='position:
absolute;top:51.35%;left:0%;width:85.33%'><span style='font-family:"Gill Sans";
font-size:250%;color:#E9EB5D'><i>ubiquitin, and pyruvate kinase</i></span></span></div>
<div class=O style='position:absolute;top:50.88%;left:5.16%;width:95.23%;
height:19.78%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D'><i>Having
ÒconfirmedÓ these known relations, we can </i></span></span><span
style='position:absolute;top:33.92%;left:0%;width:99.72%'><span
style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D'><i>now add new
members to this family: Atp6l, Gnas, </i></span></span><span style='position:
absolute;top:67.85%;left:0%;width:89.01%'><span style='font-family:"Gill Sans";
font-size:250%;color:#E9EB5D'><i>Ndr4. A thin veneer of functional genomics.</i></span></span></div>
</div>
<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=Helvetica size=3>Having worked with
WebQTL now for 30 minutes, do we know anything new? The hypothesis that we
have generated (but not validated) is that three transcripts: Atp6l, Gnas,
and Ndr4 are part of a family of genes that are coregulated in normal mouse
forebrain with App and Hsp84-1. We need to add functional and mechanistic
significance to this hypothesis to make it biologically vibrant. But from a
statiistical standpoint it is a strong inference.</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=Helvetica size=3>Please donÕt say: But
these are mere correlations. A high correlation in this context has a
biological basis. The real question is are we smart enough to understand the
web (not chain) of causality that produced the correlation. Once we
understand the web of causality, does it have utility? Very often the answer
will be NO. This will often be the case when a high correlation is generated
by linkage disequilibrium of sets of polymorphisms that modulate a set of
mechanistically separated traits. Chromosomal linkage can produce
correlations that are not mechanistic in the conventional sense used by
molecular biologists. For example, clusters<span style="mso-spacerun:
yes"> </span>of hox transcription factor genes tend to be close
physically to keratin gene clusters, and one might expect shared patterns of
variance produced by this linkage in a mapping panel, no matter how large.</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=Helvetica size=3>If Affymetrix designed
probe sets with reasonable care, if we did the experiments correctly, if we
sampled animals appropriately, then a correlation of 0.70 or higher between
transcripts in the brain tells you that these two transcripts are effectively
coupled in this set of animals under this set of conditions. More than 50%
the variance in the expression of one transcript can be predicted from the
other. That is a major piece of information that could be of significant
clinical, economic, and predictive value, whatever its causes. Yes,
correlation coefficients are noisy and have large error terms, but we have
larger n of strains coming to the rescue. Expect more than 50 BXD lines soon.</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=Helvetica size=3>This is a thin veneer of
functional genomics. It is enough to generate some marvelous hypotheses in a
semi-automated way.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>Having worked with
WebQTL now for 30 minutes, do we know anything new? The hypothesis that we
have generated (but not validated) is that three transcripts: Atp6l, Gnas,
and Ndr4 are part of a family of genes that are coregulated in normal mouse
forebrain with App and Hsp84-1. We need to add functional and mechanistic
significance to this hypothesis to make it biologically vibrant. But from a
statiistical standpoint it is a strong inference.</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=Helvetica size=2>Please donÕt say: But
these are mere correlations. A high correlation in this context has a
biological basis. The real question is are we smart enough to understand the
web (not chain) of causality that produced the correlation. Once we
understand the web of causality, does it have utility? Very often the answer
will be NO. This will often be the case when a high correlation is generated
by linkage disequilibrium of sets of polymorphisms that modulate a set of
mechanistically separated traits. Chromosomal linkage can produce
correlations that are not mechanistic in the conventional sense used by
molecular biologists. For example, clusters<span style="mso-spacerun:
yes"> </span>of hox transcription factor genes tend to be close
physically to keratin gene clusters, and one might expect shared patterns of
variance produced by this linkage in a mapping panel, no matter how large.</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=Helvetica size=2>If Affymetrix designed
probe sets with reasonable care, if we did the experiments correctly, if we
sampled animals appropriately, then a correlation of 0.70 or higher between
transcripts in the brain tells you that these two transcripts are effectively
coupled in this set of animals under this set of conditions. More than 50%
the variance in the expression of one transcript can be predicted from the
other. That is a major piece of information that could be of significant
clinical, economic, and predictive value, whatever its causes. Yes,
correlation coefficients are noisy and have large error terms, but we have
larger n of strains coming to the rescue. Expect more than 50 BXD lines soon.</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=Helvetica size=2>This is a thin veneer of
functional genomics. It is enough to generate some marvelous hypotheses in a
semi-automated way.</font><br>
</td>
</tr>
</table>
</body>
</html>
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genomics</title>
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onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.41%;left:3.31%;width:105.43%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:292;mso-text-indent-alt:
0;position:absolute;top:0%;left:1.0%;width:98.99%;height:50.6%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>2.45 billion scatter plots: </span><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>here is one of the best</span></div>
</div>
<img border=0 src="slide0012_image017.gif" style='position:absolute;top:11.3%;
left:6.62%;width:67.41%;height:82.68%'>
<div class=O style='position:absolute;top:77.56%;left:41.19%;width:8.6%;
height:7.42%'><span style='font-family:"Gill Sans";font-size:283%;color:#003399;
mso-color-index:4'><i>App</i></span><span style='font-family:"Gill Sans";
font-size:283%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><i><br>
</i></span></div>
<img border=0 src="slide0012_image018.gif" alt="Text Box: Hsp84-1"
style='position:absolute;top:36.04%;left:14.17%;width:6.88%;height:27.03%'></div>
<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=Helvetica size=3>The correlation between
App and heat shock protein 84-1 transcript is most impressive.<span
style="mso-spacerun: yes"> </span>Since WebQTL now contains total of
about 70,000 traits in the BXD strains, we could produce as many as to 70k x
35k scatter plots of this type. Since all of the<span style="mso-spacerun:
yes"> </span>correlations come for a common reference population,
none<span style="mso-spacerun: yes"> </span>of the correlations are
blantantly silly. However the great majority may be uninterpretable and a
very large number may be meaningless given the signal-to-noise ratios of some
measurements. With about 30 strains, correlations above 0.7 have a reasonably
low false positive rate.</font><br>
</td>
</tr>
</table>
</div>
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</body>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image017.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0012_image017.gif Binary files differdeleted file mode 100755 index e72a2bed..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image017.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image018.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0012_image018.gif Binary files differdeleted file mode 100755 index 7f4ca288..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0012_image018.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0012_notes_pane.htm deleted file mode 100755 index 0380a033..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0012_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
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href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>The correlation between
App and heat shock protein 84-1 transcript is most impressive.<span
style="mso-spacerun: yes"> </span>Since WebQTL now contains total of
about 70,000 traits in the BXD strains, we could produce as many as to 70k x
35k scatter plots of this type. Since all of the<span style="mso-spacerun:
yes"> </span>correlations come for a common reference population,
none<span style="mso-spacerun: yes"> </span>of the correlations are
blantantly silly. However the great majority may be uninterpretable and a
very large number may be meaningless given the signal-to-noise ratios of some
measurements. With about 30 strains, correlations above 0.7 have a reasonably
low false positive rate.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0013.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0013.htm deleted file mode 100755 index 223f93fb..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0013.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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genomics</title>
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onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
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visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.41%;left:3.31%;width:93.77%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:2.11%;width:96.46%;height:50.6%'><span
style='mso-special-format:nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";
font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>Cross-tissue type correlations</span></div>
</div>
<img border=0 src="slide0013_image019.gif" style='position:absolute;top:11.83%;
left:4.1%;width:71.52%;height:46.64%'><img border=0 src="slide0013_image020.gif"
style='position:absolute;top:60.95%;left:4.1%;width:89.93%;height:35.33%'></div>
<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=Helvetica size=3>We can compare App
expression inthe forebrain against transcript expression in hematopoietic
stem cells. Some of these correlations are significant, but it may be
difficult to discovery of shared genetic (linkage disequilibrium) or
molecular processes that give rise to these correlation.</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=Helvetica size=3>The GNF Hematopoietic
stem cell data belong to Gerald de Haan (University of Groningen) and Michael
Cooke (Genomics Institute of the Novartis Research Foundation).</font><br>
</td>
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</table>
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</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>We can compare App
expression inthe forebrain against transcript expression in hematopoietic
stem cells. Some of these correlations are significant, but it may be
difficult to discovery of shared genetic (linkage disequilibrium) or
molecular processes that give rise to these correlation.</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=Helvetica size=2>The GNF Hematopoietic
stem cell data belong to Gerald de Haan (University of Groningen) and Michael
Cooke (Genomics Institute of the Novartis Research Foundation).</font><br>
</td>
</tr>
</table>
</body>
</html>
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<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.41%;left:3.31%;width:107.81%;height:14.66%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:1.84%;width:98.15%;height:85.54%'><span
style='position:absolute;top:0%;left:0%;width:99.37%'><span style='mso-special-format:
nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:
99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Cross-modal
correlations: From mRNA to to </span></span><span style='position:absolute;
top:39.43%;left:4.75%;width:95.24%'><span style='font-size:106%;color:#E9EB5D;
mso-color-index:3'>anatomy and to behavior and pharmacology</span></span></div>
</div>
<img border=0 src="slide0014_image021.gif" style='position:absolute;top:15.37%;
left:6.62%;width:53.37%;height:34.62%'><img border=0
src="slide0014_image022.gif" style='position:absolute;top:46.81%;left:17.35%;
width:65.16%;height:53.0%'></div>
<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=Helvetica size=3>Another example, but in
this case we are generating correlations between variation in transcript
levels with a database of approximately 430 published (and unpublished)
phenotypes from BXD strains. Notice that the N of strains is variable (from
21 to 28 above). Rank order statistics is more appropriate when N is under
30.</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=Helvetica size=3>The Published Phenotypes
database was prepared by Elissa Chesler and Robert Williams from data
extracted from the literature or sent to us for inclusion by our colleagues.
We especially thank John Crabbe (Oregon HSU) and Byron Jones (Pennsylvania
SU) for providing us with large pre-compiled data tables.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>Another example, but in
this case we are generating correlations between variation in transcript
levels with a database of approximately 430 published (and unpublished)
phenotypes from BXD strains. Notice that the N of strains is variable (from
21 to 28 above). Rank order statistics is more appropriate when N is under
30.</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=Helvetica size=2>The Published Phenotypes
database was prepared by Elissa Chesler and Robert Williams from data
extracted from the literature or sent to us for inclusion by our colleagues.
We especially thank John Crabbe (Oregon HSU) and Byron Jones (Pennsylvania
SU) for providing us with large pre-compiled data tables.</font><br>
</td>
</tr>
</table>
</body>
</html>
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<meta http-equiv=Content-Type content="text/html; charset=macintosh">
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<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description
content="Jun-19-03: WebQTL link to www.webqtl.org/search.html">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--
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-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:3.0%;left:2.11%;width:96.42%;height:19.61%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232;
mso-text-indent-alt:0;position:absolute;top:0%;left:.96%;width:97.39%;
height:100.0%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-size:68%'><i>WebQTL<span style="mso-spacerun:
yes"> </span><br>
</i></span></span><span style='position:
absolute;top:32.43%;left:4.37%;width:95.76%'><span style='font-size:68%'><i>link
to <br>
</i></span></span><span style='position:absolute;top:58.55%;left:4.37%;
width:95.76%'><span style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span
style='font-size:68%;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
</div>
<div style='position:absolute;top:36.57%;left:2.51%;width:73.24%;height:45.05%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='position:absolute;top:0%;left:2.71%;width:97.28%;
height:81.96%'>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:0%;width:94.6%;height:31.57%'><span
style='position:absolute;top:0%;left:7.46%;width:92.53%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:
"numbullet3\,1";color:#FBFDB8;position:absolute;left:-8.06%;font-family:Times;
font-size:99%'>1.</span></span><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>Discovering shared expression </span></span><span
style='position:absolute;top:43.93%;left:7.46%;width:82.12%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'>patterns<br>
</span></span></div>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:41.14%;left:0%;width:84.94%;height:31.57%'><span
style='position:absolute;top:0%;left:8.31%;width:91.46%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:
"numbullet3\,2";color:#FBFDB8;position:absolute;left:-9.09%;font-family:Times;
font-size:99%'>2.</span></span><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>Discovering upstream </span></span><span style='position:
absolute;top:43.93%;left:8.31%;width:91.46%'><span style='font-size:94%;
color:#E9EB5D;mso-color-index:3'>modulators (QTLs)<br>
</span></span></div>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:82.29%;left:0%;width:100.0%;height:17.7%'><span
style='position:absolute;top:0%;left:7.06%;width:92.75%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:
"numbullet3\,3";color:#FBFDB8;position:absolute;left:-7.61%;font-family:Times;
font-size:99%'>3.</span></span><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>Discovering downstream targets</span></span></div>
</div>
</div>
<img border=0 src="slide0015_image023.gif" style='position:absolute;top:17.84%;
left:74.17%;width:23.57%;height:64.31%'>
<div class=O style='position:absolute;top:75.44%;left:74.56%;width:10.46%;
height:14.48%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:42.68%'><span
style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span
style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E;
display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:45.12%;left:0%;width:82.27%;height:54.87%'><span
style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:82.15%;left:4.1%;width:96.42%;height:18.55%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div>
<img border=0 src="slide0015_image024.gif" style='position:absolute;top:51.94%;
left:47.28%;width:26.35%;height:10.77%'></div>
<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=Helvetica size=3>Part 2: Mapping upstream
modulators or QTLs. A quantitative trait locus is a chromosomal region that
harbors one or a few polymorphic gene loci that influence a trait. We are
going to be looking for QTLs that modulate the steady state expression level
of App in the adult mouse forebrain.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>Part 2: Mapping upstream
modulators or QTLs. A quantitative trait locus is a chromosomal region that
harbors one or a few polymorphic gene loci that influence a trait. We are
going to be looking for QTLs that modulate the steady state expression level
of App in the adult mouse forebrain.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0016.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0016.htm deleted file mode 100755 index 22b9419b..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0016.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master05_background.gif" v:shapes="_x0000_s3075"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div class=O style='position:absolute;top:92.93%;left:8.74%;width:18.67%;
height:5.83%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:48.48%'><span
style='font-family:Times;font-size:117%;color:white;display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:51.51%;left:0%;width:100.0%;height:48.48%'><span
style='font-family:Times;font-size:117%;color:white;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
<div class=O style='position:absolute;top:92.93%;left:35.49%;width:29.53%;
height:5.83%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:48.48%'><span style='font-family:Times;font-size:117%;color:white;
display:none'><br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:51.51%;left:0%;width:100.0%;
height:48.48%'><span style='font-family:Times;font-size:117%;color:white;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:2.12%;left:-2.64%;width:105.82%;height:11.13%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:0%;left:0%;width:100.0%;height:88.88%'>
<div style='text-align:center;mso-line-spacing:"%0 0 0";mso-margin-left-alt:
16;mso-text-indent-alt:16;position:absolute;top:0%;left:0%;width:100.0%;
height:67.85%'><span style='font-family:Arial;font-size:267%;color:#E9EB5D'><i>How
to make recombinant inbred strains (RI)</i></span><span style='font-family:
Arial;font-size:150%;color:aqua;display:none'><br>
</span></div>
<div style='text-align:center;mso-line-spacing:"%0 0 0";mso-margin-left-alt:
16;mso-text-indent-alt:16;position:absolute;top:60.71%;left:6.25%;width:87.48%;
height:39.28%'><span style='font-family:Arial;font-size:150%;color:aqua;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<img border=0 src="slide0016_image025.gif" style='position:absolute;top:28.79%;
left:45.43%;width:18.14%;height:1.06%'><img border=0
src="slide0016_image026.gif" style='position:absolute;top:20.31%;left:28.21%;
width:1.98%;height:11.83%'>
<div style='position:absolute;top:15.01%;left:25.03%;width:19.47%;height:10.07%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:8.77%;left:6.8%;width:93.19%;
height:78.94%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>C57BL/6J (B)<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:51.11%;left:0%;width:83.21%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
</div>
<img border=0 src="slide0016_image027.gif" style='position:absolute;top:20.31%;
left:30.46%;width:1.98%;height:11.83%'>
<div style='position:absolute;top:15.01%;left:62.25%;width:16.55%;height:10.07%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:8.77%;left:8.0%;width:92.8%;
height:78.94%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J (D)<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:51.11%;left:0%;width:82.75%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
</div>
<img border=0 src="slide0016_image028.gif" style='position:absolute;top:20.31%;
left:66.62%;width:4.23%;height:11.83%'><img border=0
src="slide0016_image029.gif" style='position:absolute;top:35.51%;left:23.97%;
width:50.86%;height:1.23%'><img border=0 src="slide0016_image030.gif"
style='position:absolute;top:35.68%;left:24.1%;width:.66%;height:4.06%'><img
border=0 src="slide0016_image031.gif" style='position:absolute;top:35.68%;
left:40.92%;width:.52%;height:4.06%'><img border=0 src="slide0016_image032.gif"
style='position:absolute;top:35.68%;left:57.61%;width:.52%;height:4.06%'><img
border=0 src="slide0016_image033.gif" style='position:absolute;top:35.68%;
left:74.3%;width:.52%;height:3.88%'>
<div style='position:absolute;top:42.75%;left:5.69%;width:6.75%;height:12.72%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:8.33%;left:19.6%;width:70.58%;
height:81.94%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:49.15%'><span
style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F1<br>
</b></span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:50.84%;left:0%;width:83.33%;height:49.15%'><span
style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:lastCR;
display:none'><b><br>
</b></span></div>
</div>
</div>
<img border=0 src="slide0016_image034.gif" style='position:absolute;top:39.92%;
left:22.25%;width:4.23%;height:11.83%'><img border=0
src="slide0016_image035.gif" style='position:absolute;top:39.92%;left:38.94%;
width:4.23%;height:11.83%'><img border=0 src="slide0016_image036.gif"
style='position:absolute;top:39.92%;left:55.62%;width:4.23%;height:11.83%'><img
border=0 src="slide0016_image037.gif" style='position:absolute;top:39.39%;
left:72.84%;width:4.23%;height:11.83%'><img border=0
src="slide0016_image038.gif" style='position:absolute;top:43.46%;left:43.97%;
width:11.12%;height:3.53%'><img border=0 src="slide0016_image039.gif"
style='position:absolute;top:60.95%;left:20.66%;width:9.8%;height:3.53%'>
<div style='position:absolute;top:71.73%;left:58.41%;width:20.52%;height:27.03%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:12.41%;left:6.45%;width:87.09%;
height:82.35%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:69.84%'><span style='position:absolute;top:0%;left:0%;width:99.25%'><span
style='font-family:Arial;font-size:117%;color:#FFFF99'><b>20 generations </b></span></span><span
style='position:absolute;top:39.77%;left:0%;width:100.0%'><span
style='font-family:Arial;font-size:117%;color:#FFFF99'><b>brother-sister </b></span></span><span
style='position:absolute;top:80.68%;left:0%;width:100.0%'><span
style='font-family:Arial;font-size:117%;color:#FFFF99'><b>matings</b></span><span
style='font-family:Arial;font-size:233%;color:#FFFF99;display:none'><b><br>
</b></span></span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:73.8%;left:0%;width:100.0%;
height:26.98%'><span style='font-family:Arial;font-size:233%;color:#FFFF99;
mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</div>
</div>
<img border=0 src="slide0016_image040.gif" style='position:absolute;top:60.95%;
left:50.72%;width:9.93%;height:3.53%'><img border=0 src="slide0016_image041.gif"
style='position:absolute;top:62.72%;left:54.03%;width:4.37%;height:28.97%'><img
border=0 src="slide0016_image042.gif" style='position:absolute;top:61.13%;
left:79.86%;width:10.86%;height:3.53%'><img border=0
src="slide0016_image043.gif" style='position:absolute;top:62.36%;left:83.97%;
width:4.1%;height:28.79%'>
<div style='position:absolute;top:92.93%;left:21.72%;width:9.4%;height:10.07%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:8.77%;left:12.67%;width:84.5%;
height:78.94%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD1</span><span
style='font-family:Arial;font-size:150%;color:#484848;display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:51.11%;left:0%;width:83.33%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#484848;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:92.75%;left:51.78%;width:9.4%;height:10.07%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:8.77%;left:12.67%;width:84.5%;
height:78.94%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD2<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:51.11%;left:0%;width:83.33%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:92.93%;left:80.79%;width:10.99%;height:6.0%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:14.7%;left:12.04%;width:87.95%;
height:64.7%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD80</span></div>
</div>
<div style='position:absolute;top:90.45%;left:64.1%;width:17.74%;height:17.84%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:5.94%;left:7.46%;width:92.53%;
height:87.12%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:48.86%'><span
style='font-family:Arial;font-size:300%;color:#FFFF99'>+ É +<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:50.0%;left:0%;width:83.87%;height:48.86%'><span
style='font-family:Arial;font-size:300%;color:#FFFF99;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:62.89%;left:4.9%;width:6.75%;height:12.72%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:6.94%;left:19.6%;width:70.58%;
height:81.94%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:49.15%'><span
style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F2<br>
</b></span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:50.84%;left:0%;width:83.33%;height:49.15%'><span
style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:lastCR;
display:none'><b><br>
</b></span></div>
</div>
</div>
<img border=0 src="slide0016_image044.gif" style='position:absolute;top:54.24%;
left:18.01%;width:75.62%;height:1.06%'><img border=0
src="slide0016_image045.gif" style='position:absolute;top:54.06%;left:17.88%;
width:.66%;height:3.88%'><img border=0 src="slide0016_image046.gif"
style='position:absolute;top:54.24%;left:32.45%;width:.52%;height:3.88%'><img
border=0 src="slide0016_image047.gif" style='position:absolute;top:54.24%;
left:48.07%;width:.52%;height:4.06%'><img border=0 src="slide0016_image048.gif"
style='position:absolute;top:54.24%;left:62.78%;width:.52%;height:4.06%'><img
border=0 src="slide0016_image049.gif" style='position:absolute;top:54.24%;
left:77.74%;width:.52%;height:4.06%'><img border=0 src="slide0016_image050.gif"
style='position:absolute;top:54.59%;left:92.71%;width:.52%;height:3.71%'><img
border=0 src="slide0016_image051.gif" style='position:absolute;top:44.87%;
left:49.13%;width:.79%;height:10.07%'><img border=0 src="slide0016_image052.gif"
style='position:absolute;top:57.59%;left:15.89%;width:4.23%;height:11.83%'><img
border=0 src="slide0016_image053.gif" style='position:absolute;top:57.59%;
left:30.86%;width:4.37%;height:11.83%'><img border=0
src="slide0016_image054.gif" style='position:absolute;top:57.59%;left:46.35%;
width:4.23%;height:11.83%'><img border=0 src="slide0016_image055.gif"
style='position:absolute;top:57.59%;left:60.92%;width:4.23%;height:11.83%'><img
border=0 src="slide0016_image056.gif" style='position:absolute;top:57.59%;
left:75.62%;width:4.23%;height:11.83%'><img border=0
src="slide0016_image057.gif" style='position:absolute;top:57.59%;left:90.86%;
width:4.23%;height:11.83%'><img border=0 src="slide0016_image058.gif"
style='position:absolute;top:84.09%;left:56.42%;width:1.98%;height:1.41%'><img
border=0 src="slide0016_image059.gif" style='position:absolute;top:80.21%;
left:25.96%;width:1.98%;height:11.83%'><img border=0
src="slide0016_image060.gif" style='position:absolute;top:84.98%;left:86.09%;
width:1.85%;height:2.12%'>
<div style='position:absolute;top:75.61%;left:1.58%;width:14.17%;height:14.13%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:7.5%;left:.93%;width:97.19%;
height:83.75%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.69%;width:83.65%;
height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'><b>BXD
RI<br>
</b></span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%;
height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'><b>Strain
set<br>
</b></span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.69%;width:83.65%;
height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;
mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</div>
</div>
<img border=0 src="slide0016_image061.gif" style='position:absolute;top:12.36%;
left:14.17%;width:10.59%;height:6.36%'><img border=0
src="slide0016_image062.gif" style='position:absolute;top:10.6%;left:76.42%;
width:14.3%;height:8.3%'>
<div style='position:absolute;top:20.84%;left:17.48%;width:9.8%;height:14.13%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:7.5%;left:6.75%;width:86.48%;
height:83.75%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.81%;width:82.81%;
height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>fully<br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%;
height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>inbred<br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.81%;width:82.81%;
height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:38.16%;left:2.91%;width:12.05%;height:10.07%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:8.77%;left:3.29%;width:92.3%;
height:78.94%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>isogenic<br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:51.11%;left:8.33%;width:83.33%;
height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:54.41%;left:1.85%;width:12.45%;height:14.13%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:7.5%;left:2.12%;width:93.61%;
height:83.75%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.95%;width:82.95%;
height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>hetero-<br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%;
height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>geneous<br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.95%;width:82.95%;
height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:74.91%;left:29.0%;width:22.25%;height:22.08%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:4.0%;left:5.35%;width:88.09%;
height:90.4%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:79.64%'><span style='position:absolute;top:0%;left:.67%;width:99.32%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>Recombined </span></span><span
style='position:absolute;top:25.55%;left:.67%;width:99.32%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>chromosomes </span></span><span
style='position:absolute;top:51.11%;left:0%;width:100.0%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>are needed for </span></span><span
style='position:absolute;top:75.55%;left:.67%;width:99.32%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>mapping<br>
</span></span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:80.53%;left:.67%;width:99.32%;
height:19.46%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:10.24%;left:25.56%;width:10.46%;height:10.07%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:8.77%;left:12.65%;width:87.34%;
height:78.94%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>female<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:51.11%;left:0%;width:84.05%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:10.24%;left:64.5%;width:8.21%;height:10.07%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:8.77%;left:14.51%;width:80.64%;
height:78.94%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99'>male<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:51.11%;left:0%;width:84.0%;height:48.88%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:30.56%;left:78.01%;width:19.47%;height:10.07%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:15.78%;left:6.12%;width:93.19%;
height:71.92%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:41.46%'><span
style='font-family:Arial;font-size:117%;color:#FFFF99'>chromosome pair</span><span
style='font-family:Arial;font-size:150%;color:#FFFF99;display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:46.34%;left:0%;width:83.21%;height:53.65%'><span
style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
</div>
<img border=0 src="slide0016_image063.gif" style='position:absolute;top:31.09%;
left:65.82%;width:12.84%;height:2.82%'>
<div style='position:absolute;top:86.21%;left:3.97%;width:10.06%;height:14.48%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:4.87%;left:5.26%;width:86.84%;
height:85.36%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:9.09%;width:83.33%;
height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>Inbred<br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:25.71%;left:0%;width:100.0%;
height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>Isogenic<br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:50.0%;left:6.06%;width:90.9%;
height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>siblings</span><span
style='font-family:Arial;font-size:117%;color:aqua;display:none'><br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:75.71%;left:9.09%;width:83.33%;
height:24.28%'><span style='font-family:Arial;font-size:117%;color:aqua;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<img border=0 src="slide0016_image064.gif" style='position:absolute;top:79.32%;
left:83.7%;width:1.98%;height:11.83%'><img border=0 src="slide0016_image065.gif"
style='position:absolute;top:79.85%;left:53.5%;width:1.98%;height:11.83%'><img
border=0 src="slide0016_image066.gif" style='position:absolute;top:80.21%;
left:23.44%;width:1.98%;height:11.83%'>
<div style='position:absolute;top:18.72%;left:43.04%;width:13.77%;height:9.89%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:10.71%;left:9.61%;width:90.38%;height:76.78%'><span
style='font-family:Arial;font-size:300%;color:aqua'>B</span><span
style='font-family:Arial;font-size:300%;color:#FFFF99'>X</span><span
style='font-family:Arial;font-size:300%;color:#FF1911'>D</span></div>
</div>
<img border=0 src="slide0016_image067.gif" style='position:absolute;top:27.2%;
left:32.98%;width:31.39%;height:4.06%'><img border=0
src="slide0016_image068.gif" style='position:absolute;top:66.25%;left:60.92%;
width:1.98%;height:3.18%'><img border=0 src="slide0016_image069.gif"
style='position:absolute;top:64.31%;left:15.89%;width:1.98%;height:5.3%'><img
border=0 src="slide0016_image070.gif" style='position:absolute;top:57.59%;
left:75.62%;width:1.98%;height:5.65%'><img border=0 src="slide0016_image071.gif"
style='position:absolute;top:28.44%;left:48.87%;width:.92%;height:8.12%'><img
border=0 src="slide0016_image072.gif" style='position:absolute;top:62.19%;
left:23.84%;width:3.57%;height:16.96%'><img border=0
src="slide0016_image073.gif" style='position:absolute;top:61.48%;left:63.17%;
width:1.98%;height:8.12%'></div>
<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>The next set of slides
provide a very short interlude on QTL mapping. You will need to do some
independent reading on this topic if this is your first exposure to QTL
mapping. The recombinant inbred strains that we are using in WebQTL and in
this particular demo were generated about 25 years ago by Dr. Ben Taylor at
The Jackson Laboratory. He crossed a female C57BL/6J mouse with a male DBA/2J
mice. At the bottom of this slide we have schematized one chromosome pair
from three out of 80 BXD RI strains.<span style="mso-spacerun: yes">
</span>The dashed vertical lines that lead to the final BXD RI lines involve
20 full sib matings (about 6 years of breeding). Some lines die<span
style="mso-spacerun: yes"> </span>out during inbreeding. For example,
there is no extant BXD3 or BXD4 strain.</font><br>
</td>
</tr>
</table>
</div>
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<head>
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<td align=left colspan=1><font face=Verdana size=2>The next set of slides
provide a very short interlude on QTL mapping. You will need to do some
independent reading on this topic if this is your first exposure to QTL
mapping. The recombinant inbred strains that we are using in WebQTL and in
this particular demo were generated about 25 years ago by Dr. Ben Taylor at
The Jackson Laboratory. He crossed a female C57BL/6J mouse with a male DBA/2J
mice. At the bottom of this slide we have schematized one chromosome pair
from three out of 80 BXD RI strains.<span style="mso-spacerun: yes">
</span>The dashed vertical lines that lead to the final BXD RI lines involve
20 full sib matings (about 6 years of breeding). Some lines die<span
style="mso-spacerun: yes"> </span>out during inbreeding. For example,
there is no extant BXD3 or BXD4 strain.</font><br>
</td>
</tr>
</table>
</body>
</html>
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onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img
border=0 src="slide0017_image074.gif" style='position:absolute;top:40.45%;
left:73.24%;width:14.56%;height:5.3%'>
<div class=O style='position:absolute;top:40.81%;left:74.56%;width:11.92%;
height:7.24%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:60.97%'><span
style='font-family:Gadget;font-size:150%;color:white'>aa<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:41.46%;left:0%;width:100.0%;height:60.97%'><span
style='font-family:Gadget;font-size:150%;color:white;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
<img border=0 src="slide0017_image075.gif" style='position:absolute;top:16.6%;
left:73.24%;width:14.56%;height:5.3%'>
<div class=O style='position:absolute;top:16.96%;left:74.56%;width:11.92%;
height:7.24%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:60.97%'><span
style='font-family:Gadget;font-size:150%;color:white'>aaaa<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:41.46%;left:0%;width:100.0%;height:60.97%'><span
style='font-family:Gadget;font-size:150%;color:white;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:20.31%;left:71.65%;width:25.96%;height:19.78%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:9.82%;left:5.1%;width:95.4%;
height:83.03%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span
style='font-size:267%;color:#E2EBF0'>D2 strain</span><span style='font-family:
Palatino;font-size:333%;color:#FBFDB8;display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:49.46%;left:0%;width:88.77%;height:50.53%'><span
style='font-family:Palatino;font-size:333%;color:#FBFDB8;mso-special-format:
lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:43.81%;left:71.65%;width:25.56%;height:19.78%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:10.71%;left:5.18%;width:94.81%;
height:83.03%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span
style='font-size:267%;color:#F6BF69'>B6 strain</span><span style='font-family:
Palatino;font-size:333%;color:#F6BF69;display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:48.38%;left:0%;width:87.43%;height:50.53%'><span
style='font-family:Palatino;font-size:333%;color:#F6BF69;mso-special-format:
lastCR;display:none'><br>
</span></div>
</div>
</div>
<img border=0 src="slide0017_image076.gif" style='position:absolute;top:17.31%;
left:31.25%;width:1.32%;height:42.22%'><img border=0
src="slide0017_image077.gif" style='position:absolute;top:40.63%;left:31.39%;
width:39.86%;height:3.53%'>
<div style='position:absolute;top:17.13%;left:40.0%;width:30.59%;height:31.44%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:11.23%;left:4.32%;width:90.9%;
height:83.7%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:0%;left:0%;width:100.0%;height:61.74%'><span
style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:
233%;color:#E9EB5D'><i>amount of </i></span></span><span style='position:absolute;
top:59.78%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'><i>transcript</i></span><span
style='font-family:Palatino;font-size:367%;color:#E9EB5D;display:none'><br>
</span></span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:65.77%;left:0%;width:100.0%;height:34.89%'><span
style='font-family:Palatino;font-size:367%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:6.0%;left:72.45%;width:21.32%;height:19.78%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:9.82%;left:6.21%;width:87.57%;
height:83.03%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span
style='font-size:267%;color:white'>4 </span><span style='font-size:233%;
color:white'>units</span><span style='font-family:Palatino;font-size:333%;
color:#E9EB5D;display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:49.46%;left:0%;width:100.0%;height:50.53%'><span
style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:29.5%;left:72.45%;width:21.32%;height:19.78%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:10.71%;left:6.21%;width:87.57%;
height:83.03%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span
style='font-size:267%;color:white'>2</span><span style='font-size:233%;
color:white'> units</span><span style='font-family:Palatino;font-size:333%;
color:#E9EB5D;display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:48.38%;left:0%;width:100.0%;height:50.53%'><span
style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></div>
</div>
</div>
<img border=0 src="slide0017_image078.gif" style='position:absolute;top:15.72%;
left:31.25%;width:40.26%;height:5.47%'>
<div class=O style='position:absolute;top:17.84%;left:9.93%;width:4.76%;
height:16.43%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span
style='font-size:300%;color:#E2EBF0'>D<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:49.46%;left:0%;width:83.33%;height:50.53%'><span
style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<div class=O style='position:absolute;top:17.84%;left:17.88%;width:4.23%;
height:16.43%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span
style='font-size:300%;color:#F6BF69'>B<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:49.46%;left:0%;width:84.37%;height:50.53%'><span
style='font-size:300%;color:#F6BF69;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:77.73%;left:5.43%;width:104.37%;height:26.32%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:8.72%;left:1.26%;width:98.73%;
height:87.24%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:62.3%'><span
style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:
233%;color:#E2EBF0'>D</span><span style='font-size:233%;color:#E9EB5D'> </span><span
style='font-size:200%;color:#E9EB5D'>and </span><span style='font-size:233%;
color:#F6BF69'>B</span><span style='font-size:233%;color:#E9EB5D'> </span><span
style='font-size:200%;color:#E9EB5D'>may be SNP-like variants in the promoter </span></span><span
style='position:absolute;top:61.72%;left:0%;width:97.55%'><span
style='font-size:200%;color:#E9EB5D'>itself (cis QTL) or in </span><span
style='font-size:200%;color:#EAEC5E'>upstream genes (trans QTLs)</span><span
style='font-size:300%;color:#E9EB5D;display:none'><br>
</span></span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:63.84%;left:0%;width:86.88%;height:36.15%'><span
style='font-size:300%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<div class=O style='position:absolute;top:7.59%;left:4.23%;width:22.78%;
height:16.25%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:0%;left:1.74%;width:97.09%;
height:33.69%'><span style='font-size:200%;color:#E9EB5D'>UPSTREAM<br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:32.6%;left:0%;width:100.0%;
height:33.69%'><span style='font-size:200%;color:#E9EB5D'>modulators<br>
</span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:66.3%;left:4.65%;width:90.69%;
height:33.69%'><span style='font-size:200%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:7.59%;left:44.5%;width:17.21%;height:18.19%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:3.88%;left:6.92%;width:83.84%;
height:90.29%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span
style='font-size:300%;color:#E2EBF0'>High<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:49.46%;left:0%;width:100.0%;height:50.53%'><span
style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:63.78%;left:8.74%;width:6.62%;height:18.19%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:3.88%;left:20.0%;width:72.0%;
height:90.29%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span
style='font-size:300%;color:#E2EBF0'>D<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:49.46%;left:0%;width:83.33%;height:50.53%'><span
style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:63.78%;left:15.09%;width:6.22%;height:18.19%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:3.88%;left:19.14%;width:68.08%;
height:90.29%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span
style='font-size:300%;color:#F6BF69'>B<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:49.46%;left:0%;width:84.37%;height:50.53%'><span
style='font-size:300%;color:#F6BF69;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<div style='position:absolute;top:71.02%;left:7.54%;width:16.02%;height:12.72%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:5.55%;left:7.43%;width:91.73%;
height:86.11%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:50.0%'><span
style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span
style='font-size:200%;color:#E9EB5D;display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:48.38%;left:0%;width:82.88%;height:50.0%'><span
style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
<img border=0 src="slide0017_image079.gif" style='position:absolute;top:57.24%;
left:-1.05%;width:101.98%;height:7.59%'>
<div class=O style='position:absolute;top:44.16%;left:47.15%;width:9.4%;
height:12.72%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:51.38%'><span
style='font-size:233%;color:#F6BF69'>Low<br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:50.0%;left:0%;width:83.09%;height:51.38%'><span
style='font-size:233%;color:#F6BF69;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:58.12%;left:.79%;width:114.56%;height:6.53%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:10.81%;left:1.15%;width:98.84%;height:72.97%'><span
style='font-family:Gadget;font-size:167%;color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2
- etc-3'UTR >>>>></span></div>
</div>
<img border=0 src="slide0017_image080.gif" style='position:absolute;top:37.98%;
left:8.6%;width:13.77%;height:20.67%'>
<div class=O style='position:absolute;top:39.75%;left:10.06%;width:3.57%;
height:12.01%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white'><b><br>
</b></span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:52.94%;left:7.4%;width:85.18%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white;
mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</div>
<div class=O style='position:absolute;top:40.1%;left:17.48%;width:3.57%;
height:12.01%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white'><b><br>
</b></span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:51.47%;left:7.4%;width:85.18%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white;
mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</div>
<img border=0 src="slide0017_image081.gif" style='position:absolute;top:33.74%;
left:8.6%;width:13.77%;height:20.67%'>
<div class=O style='position:absolute;top:35.86%;left:17.48%;width:3.57%;
height:12.01%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white'><b><br>
</b></span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:51.47%;left:7.4%;width:85.18%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white;
mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</div>
<div class=O style='position:absolute;top:35.51%;left:10.06%;width:3.57%;
height:12.01%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white'><b><br>
</b></span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:51.47%;left:7.4%;width:85.18%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white;
mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</div>
<div class=O style='position:absolute;top:37.8%;left:20.66%;width:.13%;
height:12.01%'>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white;
display:none'><b><br>
</b></span></div>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:51.47%;left:0%;width:100.0%;
height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white;
mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</div>
<img border=0 src="slide0017_image082.gif" style='position:absolute;top:27.38%;
left:4.9%;width:21.45%;height:21.37%'>
<div style='position:absolute;top:27.38%;left:5.03%;width:21.05%;height:12.72%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:5.55%;left:6.28%;width:93.71%;
height:86.11%'>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:0%;left:0%;width:100.0%;height:50.0%'><span
style='font-size:200%;color:#E9EB5D'><i>trans QTL</i></span><span
style='font-size:200%;color:#E9EB5D;display:none'><br>
</span></div>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17;position:absolute;top:48.38%;left:0%;width:83.22%;height:50.0%'><span
style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
</div>
</div>
<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=Helvetica size=3>This slide is
illustrates two categories of QTLs that modulate variability in transcript
abundance.</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=Helvetica size=3>1. cis QTLs are defined
as QTLs that are closely linked to the gene whose transcript is the measured
trait. For example, a polymorphism in the promoter that affects the binding
of a transcription factor. However, cis QTLs can be far upstream or downstream
polymorphisms in enhancers. They may also be polymorphisms in neigghboring
genes.</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=Helvetica size=3>2. trans QTLs map far
enough away from the location of the gene that gives rise to the transcript
that is being measured so that we can be quite certain that the QTL is not IN
the gene itself. The most blatant type of trans-QTL would be a polymorphism
in a transcription factor. BUT in the majority of cases, the trans QTLs can
be far removed in a mechanistic sense from the actual events modulating
transcript abundance. That is why there are three overlappoing arrows above.<span
style="mso-spacerun: yes"> </span>The way in which an upstream
polymorphism influences a downstream difference in mRNA abundance can be very
indirect. Effects can :</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3><span
style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun:
yes"> </span>cross tissue types (a polymorphic liver enzyme may affect
CNS gene expression)</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3><span
style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun:
yes"> </span>cross time (the modulator is only expressed for one day
during development but has permanent effects in adults),</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3><span
style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun:
yes"> </span>may be contingent on environmental factors (heat shock may
trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>This slide is
illustrates two categories of QTLs that modulate variability in transcript
abundance.</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=Helvetica size=2>1. cis QTLs are defined
as QTLs that are closely linked to the gene whose transcript is the measured
trait. For example, a polymorphism in the promoter that affects the binding
of a transcription factor. However, cis QTLs can be far upstream or downstream
polymorphisms in enhancers. They may also be polymorphisms in neigghboring
genes.</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=Helvetica size=2>2. trans QTLs map far
enough away from the location of the gene that gives rise to the transcript
that is being measured so that we can be quite certain that the QTL is not IN
the gene itself. The most blatant type of trans-QTL would be a polymorphism
in a transcription factor. BUT in the majority of cases, the trans QTLs can
be far removed in a mechanistic sense from the actual events modulating
transcript abundance. That is why there are three overlappoing arrows above.<span
style="mso-spacerun: yes"> </span>The way in which an upstream
polymorphism influences a downstream difference in mRNA abundance can be very
indirect. Effects can :</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2><span
style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun:
yes"> </span>cross tissue types (a polymorphic liver enzyme may affect
CNS gene expression)</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2><span
style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun:
yes"> </span>cross time (the modulator is only expressed for one day
during development but has permanent effects in adults),</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2><span
style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun:
yes"> </span>may be contingent on environmental factors (heat shock may
trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br>
</td>
</tr>
</table>
</body>
</html>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
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visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:2.29%;left:4.1%;width:105.16%;height:9.01%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:11.76%;
left:1.25%;width:98.86%;height:82.35%'><span style='font-family:Verdana;
font-size:73%'><i>WebQTL to exploring upstream control</i></span></div>
</div>
<img border=0 src="slide0018_image083.gif" style='position:absolute;top:13.07%;
left:5.16%;width:89.66%;height:62.19%'><img border=0
src="slide0018_image084.gif" style='position:absolute;top:19.25%;left:55.49%;
width:19.2%;height:25.97%'>
<div class=O style='position:absolute;top:16.43%;left:74.3%;width:15.49%;
height:5.65%'><span style='font-family:"Gill Sans";font-size:217%;color:#FF0F0F'>Just
click</span></div>
</div>
<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>Back to the demo. Please
bring the Traiit Data and Editing window to the front and look for the
Interval Mapping button. Please confirm that you are back to the trait
amyloid beta precursor protein.<span style="mso-spacerun: yes">
</span>If so, then just click the button.</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>Notice that the default
for:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes)
is ALL</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Select Probes is Probe Set</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Options: Permuation test
YES<span style="mso-spacerun: yes"> </span>(1000 is the default number)</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test
YES (1000 is the default number)</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0018_image083.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0018_image083.gif Binary files differdeleted file mode 100755 index eb07999f..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0018_image083.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0018_image084.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0018_image084.gif Binary files differdeleted file mode 100755 index 32b75679..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0018_image084.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0018_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0018_notes_pane.htm deleted file mode 100755 index 50a3e6c2..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0018_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=2>Back to the demo. Please
bring the Traiit Data and Editing window to the front and look for the
Interval Mapping button. Please confirm that you are back to the trait
amyloid beta precursor protein.<span style="mso-spacerun: yes">
</span>If so, then just click the button.</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=2>Notice that the default
for:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Select Chrs (chromosomes)
is ALL</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Select Probes is Probe Set</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Options: Permuation test
YES<span style="mso-spacerun: yes"> </span>(1000 is the default number)</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Options: Bootstrap test
YES (1000 is the default number)</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0019.htm deleted file mode 100755 index 9040b37a..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0019.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:2.29%;left:4.1%;width:106.88%;height:9.01%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:233;
mso-text-indent-alt:0;position:absolute;top:11.76%;left:.99%;width:99.0%;
height:82.35%'><span style='font-family:Verdana;font-size:73%'><i>WebQTL to
exploring upstream control.</i></span></div>
</div>
<img border=0 src="slide0019_image085.gif" style='position:absolute;top:27.2%;
left:1.72%;width:96.68%;height:51.76%'>
<div class=O style='position:absolute;top:13.78%;left:19.33%;width:60.52%;
height:6.53%'><span style='font-size:233%;color:#E9EB5D'><i>App maps on Chr 16
here</i></span></div>
<img border=0 src="slide0019_image086.gif" style='position:absolute;top:15.9%;
left:68.34%;width:14.43%;height:37.98%'><img border=0
src="slide0019_image087.gif" style='position:absolute;top:53.18%;left:13.5%;
width:14.43%;height:37.98%'>
<div class=O style='position:absolute;top:82.86%;left:26.88%;width:90.59%;
height:14.48%'>
<div style='position:absolute;top:0%;left:0%;width:83.33%;height:51.21%'><span
style='font-size:267%;color:#E9EB5D'><i>Is App modulated by Chr 2?<br>
</i></span></div>
<div style='position:absolute;top:50.0%;left:0%;width:100.0%;height:51.21%'><span
style='font-size:267%;color:#E9EB5D'><i>Probably, but donÕt bet the farm. </i></span></div>
</div>
</div>
<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>This is the main output
type: a so-called full genome interval map.</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 X-axis represents all
19 autosomes and the X chromosome as if they were laid end to end with short
gaps between the telomere of one chromosome and the centromere of the next
chromosome (mouse chromsomes only have a single long arm and the centromere represents
the origin of each chromosome for numerical purpose: 0 centimorgans and
almost 0 megabases). The blue labels along the bottom of the figure list a
subset of markers that were used in mapping. We used 753 markers to perform
the mapping but here we just list five markers per chromosome.</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 thick blue wavy line
running across chromsomes summarizes the strength of association between
variation in the phenotype (App expression differences) and the two genotypes
of 753 markers and the intervals between markers (hence, interval mapping).<span
style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis
to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to
convert these values to LOD scores.<span style="mso-spacerun: yes">
</span>Or you can read them as a chi-square-like statistic.</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 red line and the red
axis to the far right provides an estimate of the effect<span
style="mso-spacerun: yes"> </span>that a QTL has on expression of App
(this estimate of the addtive effect tends to be an overestimate). If the red
line is below the X-axis then this means that the allele inherited from
C57BL/6J (B6 or B) at a particular marker is associated with higher values.
If the red line is above the X-axis then the DBA/2J allele (D2 or D) is
associated with higher traits. Multiply the additive effect size by 2 to
estimate the difference between the set of strains that have the B/B genotype
and the D/D genotype at a specific marker. For example, on Chr 2 the red
line<span style="mso-spacerun: yes"> </span>peaks at a value<span
style="mso-spacerun: yes"> </span>of about 0.25. That means that this
region of chromosome 2 is responsible for a 0.5 unit expression difference
between B/B strains and the D/D strains. Since the units are log base 2, this
is 2^0.5, or about a 41% difference in expression with the D/D group being
high.</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 yellow histogram bars:
These summarize the results of a whole-genome bootstrap of the trait that is
performed 1000 times. What is a bootstrap? A bootstrap provides you a metho
of evaluating whether results are robust. If we drop out one strain, do we
still get the same results? When mapping quantitative traits, each strain
normally gets one equally weighted vote. But inthe bootstrap procedure, we
give each strain a random weighting factor of between 0 and 1.<span
style="mso-spacerun: yes"> </span>We then remap the trait and find THE
SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example,
most bootstrap results cluster on Chr 2 under the LRS peak. That is somewhat
reassuring. But notice that a substantial number of bootstrap results prefer
Chr 7 or Chr 18.</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 horizontal dashed
lines at 9.6 and 15.9. These lines are the LRS values associated with the
suggestive and significant false positive rates for genome-wide scans
established by permuations of phenotypes across genotypes. We shuffle
randomly 1000 times and obtain a distribution of peak LRS scores to generate
a null distribution. Five percent of the time, one of these permuted data
sets will have a peak LRS higher than 15.9. We call that level the 0.05
significance threshold for a whole genome scan. The p = 0.67 point is the the
suggestive level, and corresponds to the green dashed line.<span
style="mso-spacerun: yes"> </span>These thresholds are conservative for
transcripts that have expression variation that is highly heritable. The
putative or suggestive QTL on Chr 2 is probably more than just suggestive.</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>One other point: the
mapping procedure we use is computationally very fast, but it is relatively
simple. We are not looking for gene-gene interactions and we are not fitting
multiple QTLs in combinations.<span style="mso-spacerun: yes">
</span>Consider this QTL analysis a first pass that will highlight hot spots
and warm spots that are worth following up on using more sophisticated
models.</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>CLICKABLE REGIONS:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>1. If you click on the
Chromosome number then you will generate a new map just for that chromosome.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. If you click on the
body of the map, say on the blue line, then you will generate a view<span
style="mso-spacerun: yes"> </span>on a 10 Mb window of that part of the
genome from the UCSC Genome Browser web site.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. If you click on a
marker symbol, then you will generate a new Trait data and editing window
with the genotypes loaded into the window just like any other trait. More on
this later.</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>NOTE: you can drag these
maps off of the browser window and onto your desktop. The will be saved as
PNG or PDF files. You can import them into Photoshop or other programs.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image085.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image085.gif Binary files differdeleted file mode 100755 index 03a2878d..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image085.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image086.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image086.gif Binary files differdeleted file mode 100755 index 3327e4da..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image086.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image087.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0019_image087.gif Binary files differdeleted file mode 100755 index 227fce55..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0019_image087.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0019_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0019_notes_pane.htm deleted file mode 100755 index cbe88cf0..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0019_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=2>This is the main output
type: a so-called full genome interval map.</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=2>The X-axis represents all
19 autosomes and the X chromosome as if they were laid end to end with short
gaps between the telomere of one chromosome and the centromere of the next
chromosome (mouse chromsomes only have a single long arm and the centromere represents
the origin of each chromosome for numerical purpose: 0 centimorgans and
almost 0 megabases). The blue labels along the bottom of the figure list a
subset of markers that were used in mapping. We used 753 markers to perform
the mapping but here we just list five markers per chromosome.</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=2>The thick blue wavy line
running across chromsomes summarizes the strength of association between
variation in the phenotype (App expression differences) and the two genotypes
of 753 markers and the intervals between markers (hence, interval mapping).<span
style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis
to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to
convert these values to LOD scores.<span style="mso-spacerun: yes">
</span>Or you can read them as a chi-square-like statistic.</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=2>The red line and the red
axis to the far right provides an estimate of the effect<span
style="mso-spacerun: yes"> </span>that a QTL has on expression of App
(this estimate of the addtive effect tends to be an overestimate). If the red
line is below the X-axis then this means that the allele inherited from
C57BL/6J (B6 or B) at a particular marker is associated with higher values.
If the red line is above the X-axis then the DBA/2J allele (D2 or D) is
associated with higher traits. Multiply the additive effect size by 2 to
estimate the difference between the set of strains that have the B/B genotype
and the D/D genotype at a specific marker. For example, on Chr 2 the red
line<span style="mso-spacerun: yes"> </span>peaks at a value<span
style="mso-spacerun: yes"> </span>of about 0.25. That means that this
region of chromosome 2 is responsible for a 0.5 unit expression difference
between B/B strains and the D/D strains. Since the units are log base 2, this
is 2^0.5, or about a 41% difference in expression with the D/D group being
high.</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=2>The yellow histogram bars:
These summarize the results of a whole-genome bootstrap of the trait that is
performed 1000 times. What is a bootstrap? A bootstrap provides you a metho
of evaluating whether results are robust. If we drop out one strain, do we
still get the same results? When mapping quantitative traits, each strain
normally gets one equally weighted vote. But inthe bootstrap procedure, we
give each strain a random weighting factor of between 0 and 1.<span
style="mso-spacerun: yes"> </span>We then remap the trait and find THE
SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example,
most bootstrap results cluster on Chr 2 under the LRS peak. That is somewhat
reassuring. But notice that a substantial number of bootstrap results prefer
Chr 7 or Chr 18.</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=2>The horizontal dashed
lines at 9.6 and 15.9. These lines are the LRS values associated with the
suggestive and significant false positive rates for genome-wide scans
established by permuations of phenotypes across genotypes. We shuffle
randomly 1000 times and obtain a distribution of peak LRS scores to generate
a null distribution. Five percent of the time, one of these permuted data
sets will have a peak LRS higher than 15.9. We call that level the 0.05
significance threshold for a whole genome scan. The p = 0.67 point is the the
suggestive level, and corresponds to the green dashed line.<span
style="mso-spacerun: yes"> </span>These thresholds are conservative for
transcripts that have expression variation that is highly heritable. The
putative or suggestive QTL on Chr 2 is probably more than just suggestive.</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=2>One other point: the
mapping procedure we use is computationally very fast, but it is relatively
simple. We are not looking for gene-gene interactions and we are not fitting
multiple QTLs in combinations.<span style="mso-spacerun: yes">
</span>Consider this QTL analysis a first pass that will highlight hot spots
and warm spots that are worth following up on using more sophisticated
models.</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=2>CLICKABLE REGIONS:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>1. If you click on the
Chromosome number then you will generate a new map just for that chromosome.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2. If you click on the
body of the map, say on the blue line, then you will generate a view<span
style="mso-spacerun: yes"> </span>on a 10 Mb window of that part of the
genome from the UCSC Genome Browser web site.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>3. If you click on a
marker symbol, then you will generate a new Trait data and editing window
with the genotypes loaded into the window just like any other trait. More on
this later.</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=2>NOTE: you can drag these
maps off of the browser window and onto your desktop. The will be saved as
PNG or PDF files. You can import them into Photoshop or other programs.</font><br>
</td>
</tr>
</table>
</body>
</html>
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onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:2.29%;left:4.1%;width:105.82%;height:9.01%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:11.76%;
left:1.25%;width:98.87%;height:82.35%'><span style='font-family:Verdana;
font-size:73%'><i>The whole neighborhood is modulated!</i></span></div>
</div>
<img border=0 src="slide0020_image088.gif" style='position:absolute;top:13.07%;
left:9.53%;width:80.79%;height:80.38%'></div>
<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>App has a suggestive QTL
on Chr 2. What about the neighbors that we defined as having shared
expression patterns. This figure shows that members of the immediate App
neigborhood share a weak Chr 2 QTL.<span style="mso-spacerun: yes">
</span>That is what the blue oval in the background is meant to represent.
But some transcripts, such as Ndr4 and Psen2 do not share this Chr 2
interval.</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>QUESTION: What kind of
headway can we make in detemining what polymorphism or polymorphisms on Chr 2
near 130 Mb might contribute to the variance in the expression of all of
these important transcripts?</font><br>
</td>
</tr>
</table>
</div>
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<head>
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</head>
<body bgcolor=black text=white>
<table 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=2>App has a suggestive QTL
on Chr 2. What about the neighbors that we defined as having shared
expression patterns. This figure shows that members of the immediate App
neigborhood share a weak Chr 2 QTL.<span style="mso-spacerun: yes">
</span>That is what the blue oval in the background is meant to represent.
But some transcripts, such as Ndr4 and Psen2 do not share this Chr 2
interval.</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=2>QUESTION: What kind of
headway can we make in detemining what polymorphism or polymorphisms on Chr 2
near 130 Mb might contribute to the variance in the expression of all of
these important transcripts?</font><br>
</td>
</tr>
</table>
</body>
</html>
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onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:2.29%;left:4.1%;width:93.9%;height:9.01%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:11.76%;
left:1.41%;width:97.03%;height:82.35%'><span style='font-family:Verdana;
font-size:73%'><i>Which gene is the QTL?</i></span></div>
</div>
<img border=0 src="slide0021_image089.gif" style='position:absolute;top:13.07%;
left:5.03%;width:58.27%;height:37.98%'><img border=0
src="slide0021_image090.gif" style='position:absolute;top:46.81%;left:3.31%;
width:68.87%;height:51.94%'><img border=0 src="slide0021_image091.gif"
style='position:absolute;top:38.51%;left:55.62%;width:24.76%;height:25.08%'>
<div class=O style='position:absolute;top:7.77%;left:75.09%;width:21.05%;
height:28.97%'>
<div style='text-align:center;position:absolute;top:0%;left:8.17%;width:83.64%;
height:25.6%'><span style='font-size:267%;color:#E9EB5D'><i>Right <br>
</i></span></div>
<div style='text-align:center;position:absolute;top:25.0%;left:0%;width:100.0%;
height:25.6%'><span style='font-size:267%;color:#E9EB5D'><i>position<br>
</i></span></div>
<div style='text-align:center;position:absolute;top:50.0%;left:8.17%;
width:83.64%;height:25.6%'><span style='font-size:267%;color:#E9EB5D'><i>&<br>
</i></span></div>
<div style='text-align:center;position:absolute;top:75.0%;left:8.17%;
width:83.64%;height:25.6%'><span style='font-size:267%;color:#E9EB5D'><i>high r</i></span></div>
</div>
<div class=O style='position:absolute;top:50.7%;left:72.58%;width:28.87%;
height:14.48%'>
<div style='text-align:center;position:absolute;top:0%;left:8.71%;width:83.48%;
height:51.21%'><span style='font-size:267%;color:#E9EB5D'><i>good<br>
</i></span></div>
<div style='text-align:center;position:absolute;top:50.0%;left:0%;width:100.0%;
height:51.21%'><span style='font-size:267%;color:#E9EB5D'><i>candidates</i></span></div>
</div>
</div>
<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="Times New Roman" size=4><b>Candidate
Genes: </b><span style="mso-spacerun: yes"> </span>The best we can do at
this point is to make an educated guess about the candidacy status of all
genes in the QTL support interval. For sake of argument, lets say that we are
confident that the polymorphism is located between 130 and 150 Mb (20 Mb,
equivalent to roughly 10 cM). There will typically be 12 to 15 genes per Mb,
so we now would like to evaluate 240 to 300 positional candidates. We would
like to highlight the biologically relevant subset of candidates. We could
look through gene ontologies and expression levels to help us winnow the
list. An alternate way avaiable using WebQTL is to generate a list of those
genes in this 20 Mb interval that have transcripts that co-vary in expression
with App expression.</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 New Roman" size=4>To do this, go
back to the Trait Data and Editing window. Sort the correlations by position.
Select Return = 500. Then scroll down the list to see positional candidates
that share expression with App.</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 New Roman" size=4>There are
several candidates that have high correlation with App even in this short 20
Mb interval. We can rank them by correlation, but they are all close.<span
style="mso-spacerun: yes"> </span>There is one other imporant approach
to ranking these candidates. Are they likely to contain polymorphisms? We can
assess the likelihood that they contain polymorphisms by mapping each
transcript to see if any have strong cis QTLs. The logic of this search is
that a transcript that has a strong cis-QTL is likely to contain functional
polymorphisms that effect its own expression. This make is more like that the
transcript is a ÒcausativeÓ factor since it is likely to be polymorphic.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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="Times New Roman" size=4><b>Candidate
Genes: </b><span style="mso-spacerun: yes"> </span>The best we can do at
this point is to make an educated guess about the candidacy status of all
genes in the QTL support interval. For sake of argument, lets say that we are
confident that the polymorphism is located between 130 and 150 Mb (20 Mb,
equivalent to roughly 10 cM). There will typically be 12 to 15 genes per Mb,
so we now would like to evaluate 240 to 300 positional candidates. We would
like to highlight the biologically relevant subset of candidates. We could
look through gene ontologies and expression levels to help us winnow the
list. An alternate way avaiable using WebQTL is to generate a list of those
genes in this 20 Mb interval that have transcripts that co-vary in expression
with App expression.</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 New Roman" size=4>To do this, go
back to the Trait Data and Editing window. Sort the correlations by position.
Select Return = 500. Then scroll down the list to see positional candidates
that share expression with App.</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 New Roman" size=4>There are
several candidates that have high correlation with App even in this short 20
Mb interval. We can rank them by correlation, but they are all close.<span
style="mso-spacerun: yes"> </span>There is one other imporant approach
to ranking these candidates. Are they likely to contain polymorphisms? We can
assess the likelihood that they contain polymorphisms by mapping each
transcript to see if any have strong cis QTLs. The logic of this search is
that a transcript that has a strong cis-QTL is likely to contain functional
polymorphisms that effect its own expression. This make is more like that the
transcript is a ÒcausativeÓ factor since it is likely to be polymorphic.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0022.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0022.htm deleted file mode 100755 index 014925b5..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0022.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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height:4.5in !important;
font-size:76% !important;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--
-gId="slide0022.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.59%;left:3.97%;width:104.1%;height:13.78%;
filter:DropShadow(Color=#000000, OffX=4, OffY=4)'>
<div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:1.28%;left:1.27%;width:98.72%;height:88.46%'><span
style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:
233%;color:#E9EB5D'><i>Only one of these candidates is a functional </i></span></span><span
style='position:absolute;top:46.37%;left:0%;width:85.69%'><span
style='font-size:233%;color:#E9EB5D'><i>polymorphism</i></span></span></div>
</div>
<img border=0 src="slide0022_image092.gif" style='position:absolute;top:15.54%;
left:2.64%;width:41.98%;height:84.45%'><img border=0
src="slide0022_image093.gif" style='position:absolute;top:31.44%;left:26.09%;
width:27.15%;height:5.83%'>
<div class=O style='position:absolute;top:28.09%;left:54.3%;width:50.06%;
height:21.73%'>
<div style='position:absolute;top:0%;left:0%;width:100.0%;height:25.2%'><span
style='font-size:200%;color:#E9EB5D'><i>Hars2 = 0610006H08Rik<br>
</i></span></div>
<span style='position:absolute;top:24.39%;left:0%;width:94.7%'><span
style='font-size:200%;color:#E9EB5D'><i>is a cis-QTL with a very </i></span></span><span
style='position:absolute;top:49.59%;left:0%;width:84.39%'><span
style='font-size:200%;color:#E9EB5D'><i>high likelihood ratio </i></span></span><span
style='position:absolute;top:73.98%;left:0%;width:84.39%'><span
style='font-size:200%;color:#E9EB5D'><i>statistic (LRS) score</i></span><span
style='font-size:267%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
</div>
<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=Helvetica size=3>When you do this you
will find that only the transcript 0610006H08Rik has a strong cis QTL. See
the slide above. The LRS peaks above 35<span style="mso-spacerun: yes">
</span>(LOD of greater than 7.5). It turns out that this transcript is really
Hars2, also known as histydl tRNA synthase 2.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>When you do this you
will find that only the transcript 0610006H08Rik has a strong cis QTL. See
the slide above. The LRS peaks above 35<span style="mso-spacerun: yes">
</span>(LOD of greater than 7.5). It turns out that this transcript is really
Hars2, also known as histydl tRNA synthase 2.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0023.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0023.htm deleted file mode 100755 index dac0fddc..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0023.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Jun-19-03>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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-gId="slide0023.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:1.59%;left:3.97%;width:104.1%;height:8.12%;
filter:DropShadow(Color=#000000, OffX=4, OffY=4)'>
<div class=O style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:2.17%;left:1.27%;width:98.85%;height:80.43%'><span
style='font-size:233%;color:#E9EB5D'><i>Hars2 probe level analysis: 16 PMs
mapped</i></span></div>
</div>
<img border=0 src="slide0023_image094.gif" style='position:absolute;top:10.77%;
left:13.64%;width:72.58%;height:84.8%'><img border=0
src="slide0023_image095.gif" style='position:absolute;top:59.18%;left:2.38%;
width:41.05%;height:36.74%'><img border=0 src="slide0023_image096.gif"
style='position:absolute;top:60.07%;left:36.82%;width:26.75%;height:19.08%'><img
border=0 src="slide0023_image097.gif" style='position:absolute;top:33.39%;
left:21.19%;width:64.37%;height:2.65%'><img border=0
src="slide0023_image098.gif" style='position:absolute;top:35.68%;left:21.19%;
width:64.37%;height:2.65%'><img border=0 src="slide0023_image099.gif"
style='position:absolute;top:38.33%;left:21.19%;width:64.37%;height:2.65%'><img
border=0 src="slide0023_image100.gif" style='position:absolute;top:19.78%;
left:20.79%;width:28.74%;height:21.73%'>
<div class=O style='position:absolute;top:28.09%;left:30.06%;width:4.9%;
height:3.35%'><span style='font-size:117%;color:#FF0F0F'><i>SNP</i></span></div>
<div class=O style='mso-line-spacing:"100 50 0";position:absolute;top:29.15%;
left:40.13%;width:18.67%;height:3.35%'><span style='font-size:117%;color:#FF0F0F'>C
in B6, T in D2 </span><span style='font-size:150%;color:black;mso-special-format:
lastCR;display:none'><b><br>
</b></span></div>
<div class=O style='position:absolute;top:36.39%;left:50.99%;width:9.8%;
height:3.35%'><span style='font-size:117%;color:#003399;mso-color-index:4'><i>no
SNPs</i></span></div>
</div>
<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=Helvetica size=3>LetÕs look at Hars2 in
more detail by mapping all of the perfect match probes (16 of them) that
target this transcript.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Go back to the Trait
Data and Editing window and select Chr 2 (rather than ALL as shown above) and
also select PM Probes. Then click on Interval Mapping button.</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=Helvetica size=3>You will get the
illustration above, but without the sequence data that we have added.<span
style="mso-spacerun: yes"> </span>The 16 perfect match probes are
arranged in sequence (red is 5 prime, blue is the 3 prime end). For example,
the 5 prime-most primer 307387 has the sequence CACTG..... It also has a
polymorphism at the 17 nucleotide of this 25 nt probe sequence.</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=Helvetica size=3>How do we know that the
5 prime probe is polymorphic? By looking up the sequence in the Celera
Genomics databases which often contqains sequence data for C57BL/6J (B6
above) and for DBA/2J.<span style="mso-spacerun: yes"> </span>But two
blue probes (14 and 15) do NOT contain SNPs but still have very large LRS
scores. The other probes do not perform so wel. Highly variable probe
performance is probably a result of the very different stacking energies of
DNA-RNA duplexes.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>LetÕs look at Hars2 in
more detail by mapping all of the perfect match probes (16 of them) that
target this transcript.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Go back to the Trait
Data and Editing window and select Chr 2 (rather than ALL as shown above) and
also select PM Probes. Then click on Interval Mapping button.</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=Helvetica size=2>You will get the
illustration above, but without the sequence data that we have added.<span
style="mso-spacerun: yes"> </span>The 16 perfect match probes are
arranged in sequence (red is 5 prime, blue is the 3 prime end). For example,
the 5 prime-most primer 307387 has the sequence CACTG..... It also has a
polymorphism at the 17 nucleotide of this 25 nt probe sequence.</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=Helvetica size=2>How do we know that the
5 prime probe is polymorphic? By looking up the sequence in the Celera
Genomics databases which often contqains sequence data for C57BL/6J (B6
above) and for DBA/2J.<span style="mso-spacerun: yes"> </span>But two
blue probes (14 and 15) do NOT contain SNPs but still have very large LRS
scores. The other probes do not perform so wel. Highly variable probe
performance is probably a result of the very different stacking energies of
DNA-RNA duplexes.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0024.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0024.htm deleted file mode 100755 index 4c701e50..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0024.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
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border=0 src="slide0024_image101.gif"
alt="Text Box: Tissue differences in probe performance" style='position:absolute;
top:0%;left:-.79%;width:8.21%;height:89.92%'><img border=0
src="slide0024_image102.gif" style='position:absolute;top:58.48%;left:6.88%;
width:62.78%;height:39.22%'>
<div class=O style='position:absolute;top:17.66%;left:74.3%;width:21.32%;
height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'><i>Forebrain</i></span></div>
<div class=O style='position:absolute;top:79.5%;left:74.3%;width:22.64%;
height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'><i>Stem
cells</i></span></div>
<img border=0 src="slide0024_image103.gif" style='position:absolute;top:28.97%;
left:6.75%;width:62.78%;height:36.21%'><img border=0
src="slide0024_image104.gif" style='position:absolute;top:0%;left:6.62%;
width:63.04%;height:36.39%'>
<div class=O style='position:absolute;top:51.06%;left:73.5%;width:25.56%;
height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'><i>Cerebellum</i></span></div>
</div>
<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>The vertical text says it
all: Even when using identical probes, mapping performance (and signal)
depends on tissue type and mRNA complexity. This is another gene in the Hars2
interval. Forebrain and tem cell mRNAs were run on the same U74Av2 array,
whereas the cerebellum mRNA was run on the 430A and 430B array set.</font><br>
</td>
</tr>
</table>
</div>
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<head>
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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<body bgcolor=black text=white>
<table border=0 width="100%">
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<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>The vertical text says it
all: Even when using identical probes, mapping performance (and signal)
depends on tissue type and mRNA complexity. This is another gene in the Hars2
interval. Forebrain and tem cell mRNAs were run on the same U74Av2 array,
whereas the cerebellum mRNA was run on the 430A and 430B array set.</font><br>
</td>
</tr>
</table>
</body>
</html>
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<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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content="Jun-19-03: Is there known biology to link Hars2 with App? ">
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:-3.53%;left:2.11%;width:96.42%;height:18.55%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232;
mso-text-indent-alt:0;position:absolute;top:30.47%;left:.96%;width:97.39%;
height:35.23%'><span style='font-size:68%'><i>Is there known biology to link
Hars2 with App? </i></span></div>
</div>
<div style='position:absolute;top:82.15%;left:4.1%;width:96.42%;height:18.55%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div>
<div class=O style='position:absolute;top:62.54%;left:5.16%;width:29.13%;
height:12.36%'>
<div style='position:absolute;top:0%;left:0%;width:100.0%;height:34.28%'><span
style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>69 SNPs, 1 cSNP:
<br>
</b></span></div>
<div style='position:absolute;top:32.85%;left:0%;width:96.81%;height:34.28%'><span
style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>6 exons in NCBI,
<br>
</b></span></div>
<div style='position:absolute;top:65.71%;left:0%;width:100.0%;height:34.28%'><span
style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>2 exons in Celera</b></span></div>
</div>
<img border=0 src="slide0025_image105.gif" style='position:absolute;top:9.54%;
left:3.31%;width:60.79%;height:42.57%'><img border=0
src="slide0025_image106.gif" style='position:absolute;top:28.62%;left:40.0%;
width:55.76%;height:69.78%'>
<div class=O style='position:absolute;top:14.13%;left:69.4%;width:23.84%;
height:6.53%'><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D'><i><span
style="mso-spacerun: yes"> </span>Not obvious</i></span></div>
</div>
<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=Helvetica size=3>Hars2 is not a well
characterized gene and their is no biology yet to support the hypothesis that
Hars2 modulates gene expression, let alone App expression in specific. There
are also serious database/assembly discrepancies between Celera and MGSCv3
regarding the genomic organization of this gene. But there appear to be
approximately 69 SNPs in Hars2, one of which results in a substitution.</font><br>
</td>
</tr>
</table>
</div>
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-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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<body bgcolor=black text=white>
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<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Hars2 is not a well
characterized gene and their is no biology yet to support the hypothesis that
Hars2 modulates gene expression, let alone App expression in specific. There
are also serious database/assembly discrepancies between Celera and MGSCv3
regarding the genomic organization of this gene. But there appear to be
approximately 69 SNPs in Hars2, one of which results in a substitution.</font><br>
</td>
</tr>
</table>
</body>
</html>
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<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
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<meta name=Description
content="Jun-19-03: WebQTL link to www.webqtl.org/search.html">
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:3.0%;left:2.11%;width:96.42%;height:19.61%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";mso-margin-left-alt:232;
mso-text-indent-alt:0;position:absolute;top:0%;left:.96%;width:97.39%;
height:100.0%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-size:68%'><i>WebQTL<span style="mso-spacerun:
yes"> </span><br>
</i></span></span><span style='position:
absolute;top:32.43%;left:4.37%;width:95.76%'><span style='font-size:68%'><i>link
to <br>
</i></span></span><span style='position:absolute;top:58.55%;left:4.37%;
width:95.76%'><span style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span
style='font-size:68%;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
</div>
<div style='position:absolute;top:36.57%;left:2.51%;width:73.24%;height:45.05%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='position:absolute;top:0%;left:2.71%;width:97.28%;
height:81.96%'>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:0%;width:94.6%;height:31.57%'><span
style='position:absolute;top:0%;left:7.46%;width:92.53%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:
"numbullet3\,1";color:#FBFDB8;position:absolute;left:-8.06%;font-family:Times;
font-size:99%'>1.</span></span><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>Discovering shared expression </span></span><span
style='position:absolute;top:43.93%;left:7.46%;width:82.12%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'>patterns<br>
</span></span></div>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:41.14%;left:0%;width:84.94%;height:31.57%'><span
style='position:absolute;top:0%;left:8.31%;width:91.46%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:
"numbullet3\,2";color:#FBFDB8;position:absolute;left:-9.09%;font-family:Times;
font-size:99%'>2.</span></span><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>Discovering upstream </span></span><span style='position:
absolute;top:43.93%;left:8.31%;width:91.46%'><span style='font-size:94%;
color:#E9EB5D;mso-color-index:3'>modulators (QTLs)<br>
</span></span></div>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:82.29%;left:0%;width:100.0%;height:17.7%'><span
style='position:absolute;top:0%;left:7.06%;width:92.75%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:
"numbullet3\,3";color:#FBFDB8;position:absolute;left:-7.61%;font-family:Times;
font-size:99%'>3.</span></span><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>Discovering downstream targets</span></span></div>
</div>
</div>
<div style='position:absolute;top:82.15%;left:4.1%;width:96.42%;height:18.55%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div>
<img border=0 src="slide0026_image107.gif" style='position:absolute;top:65.9%;
left:65.29%;width:26.35%;height:10.77%'></div>
<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=Helvetica size=3>Part 3.<span
style="mso-spacerun: yes"> </span>Many investigators would like to
discover the set of downstream targets of a gene of interest.</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=Helvetica size=3>In a genetic and
functional sense, that question can only be addressed effectively if there is
genetic variation in the particular gene.<span style="mso-spacerun:
yes"> </span>We know that Fos is an important transcription factor, but
unless it is polymorphic between C57BL/6J and DBA/2J, then it cannot generate
a genetic variance signal with which we can work. We can still study
covariance of Fos and hundreds of other transcripts (an interesting
exercise), but there are no genetic causes-and-effects.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=Helvetica size=2>Part 3.<span
style="mso-spacerun: yes"> </span>Many investigators would like to
discover the set of downstream targets of a gene of interest.</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=Helvetica size=2>In a genetic and
functional sense, that question can only be addressed effectively if there is
genetic variation in the particular gene.<span style="mso-spacerun:
yes"> </span>We know that Fos is an important transcription factor, but
unless it is polymorphic between C57BL/6J and DBA/2J, then it cannot generate
a genetic variance signal with which we can work. We can still study
covariance of Fos and hundreds of other transcripts (an interesting
exercise), but there are no genetic causes-and-effects.</font><br>
</td>
</tr>
</table>
</body>
</html>
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<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:7.47%;
left:1.22%;width:98.77%;height:85.04%'><span style='position:absolute;
top:0%;left:0%;width:100.0%'><span style='font-size:82%'><i>Requirement: The
gene must be polymorphic to </i></span></span><span style='position:absolute;
top:51.64%;left:3.7%;width:79.72%'><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></div>
</div>
<div style='position:absolute;top:21.37%;left:2.51%;width:84.5%;height:15.01%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:32.94%;
left:1.56%;width:98.43%;height:40.0%'><span style='font-size:64%'><i>What are
targets of the Hars2 polymorphisms?</i></span><span style='font-size:82%;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<img border=0 src="slide0027_image108.gif" style='position:absolute;top:33.92%;
left:1.72%;width:49.66%;height:32.15%'><img border=0
src="slide0027_image109.gif" style='position:absolute;top:33.39%;left:53.37%;
width:44.23%;height:58.65%'>
<div class=O style='position:absolute;top:69.96%;left:7.54%;width:51.39%;
height:21.2%'>
<div style='position:absolute;top:0%;left:0%;width:84.02%;height:32.5%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App and many
other<br>
</i></span></div>
<span style='position:absolute;top:33.33%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>correlated
transcripts and </i></span></span><span style='position:absolute;top:67.5%;
left:0%;width:84.02%'><span style='font-family:"Gill Sans";font-size:267%;
color:#E9EB5D'><i>other traits.</i></span></span></div>
</div>
<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"> </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>
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-function playList() { - -} -//-->
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</body>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0027_image108.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0027_image108.gif Binary files differdeleted file mode 100755 index c4a27e18..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0027_image108.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0027_image109.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0027_image109.gif Binary files differdeleted file mode 100755 index c03ea994..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0027_image109.gif +++ /dev/null diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0027_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0027_notes_pane.htm deleted file mode 100755 index 9614c538..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0027_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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<body bgcolor=black text=white>
<table 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=2>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=2>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=2>1.</font><font face=Verdana
size=2> 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=2>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=2>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=2>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"> </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=2>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>
</body>
</html>
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<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:16.66%;
left:1.2%;width:98.79%;height:66.66%'><span style='font-size:82%'><i>Direct
correlations between genotypes and traits</i></span><span style='font-size:
82%;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<div class=O style='position:absolute;top:22.43%;left:3.44%;width:34.83%;
height:42.4%'>
<div style='position:absolute;top:0%;left:0%;width:100.0%;height:16.25%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App and<br>
</i></span></div>
<span style='position:absolute;top:16.66%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>correlated
traits </i></span></span><span style='position:absolute;top:33.33%;left:0%;
width:100.0%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>would
be obvious </i></span></span><span style='position:absolute;top:50.0%;
left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:267%;
color:#E9EB5D'><i>candidates to </i></span></span><span style='position:absolute;
top:67.08%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";
font-size:267%;color:#E9EB5D'><i>correlate with </i></span></span><span
style='position:absolute;top:83.75%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>D2Mit423</i></span></span></div>
<img border=0 src="slide0028_image110.gif" style='position:absolute;top:10.07%;
left:33.37%;width:40.0%;height:87.63%'><img border=0
src="slide0028_image111.gif" style='position:absolute;top:82.68%;left:65.29%;
width:14.7%;height:7.24%'>
<div class=O style='position:absolute;top:79.68%;left:82.11%;width:13.11%;
height:13.95%'>
<div style='position:absolute;top:0%;left:0%;width:100.0%;height:49.36%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>B = -1<br>
</i></span></div>
<div style='position:absolute;top:50.63%;left:0%;width:94.94%;height:49.36%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>D = 1</i></span></div>
</div>
</div>
<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>We can review the set of
correlations between the marker D2Mit423 and all transcripts in
forebrain.<span style="mso-spacerun: yes"> </span>This is in essence a
backwards way of mapping QTLs. We are considering one marker and asking what
traits correlate to the marker and how well.</font><br>
</td>
</tr>
</table>
</div>
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<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>We can review the set of
correlations between the marker D2Mit423 and all transcripts in
forebrain.<span style="mso-spacerun: yes"> </span>This is in essence a
backwards way of mapping QTLs. We are considering one marker and asking what
traits correlate to the marker and how well.</font><br>
</td>
</tr>
</table>
</body>
</html>
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filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:16.66%;
left:1.36%;width:98.77%;height:66.66%'><span style='font-size:82%'><i>WhatÕs
downstream of Chr 2 near Hars2?</i></span><span style='font-size:82%;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<img border=0 src="slide0029_image112.gif" style='position:absolute;top:9.54%;
left:1.98%;width:83.04%;height:79.5%'>
<div style='position:absolute;top:86.92%;left:2.51%;width:111.12%;height:11.66%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:27.27%;
left:1.19%;width:98.8%;height:51.51%'><span style='font-size:64%'><i>Notice
many Chr 2 hits: Linkage disequilibrium limits specificity</i></span><span
style='font-size:64%;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<img border=0 src="slide0029_image113.gif" style='position:absolute;top:27.03%;
left:7.01%;width:22.38%;height:17.49%'>
<div class=O style='position:absolute;top:24.73%;left:27.68%;width:16.82%;
height:4.24%'><span style='font-size:150%;color:#FF0F0F'><b>Click here</b></span></div>
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left:48.21%;width:12.18%;height:5.47%'></div>
<div id=NotesObj style='display:none'>
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<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>The marker D2Mit423
correlates moderately well with a number of Chr 2 transcripts. This is due to
linkage disequilibrium. These correlations are not due to a molecular
interactions other than being close together on a chromosome.<span
style="mso-spacerun: yes"> </span>But we have circled one transcript,
actinin alpha 2, that has a moderately good correlation (0.59) with D2Mit423.
If we map this gene we expect to find a suggestive QTL that peaks near
D2Mit423</font><br>
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</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=2>The marker D2Mit423
correlates moderately well with a number of Chr 2 transcripts. This is due to
linkage disequilibrium. These correlations are not due to a molecular
interactions other than being close together on a chromosome.<span
style="mso-spacerun: yes"> </span>But we have circled one transcript,
actinin alpha 2, that has a moderately good correlation (0.59) with D2Mit423.
If we map this gene we expect to find a suggestive QTL that peaks near
D2Mit423</font><br>
</td>
</tr>
</table>
</body>
</html>
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<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description
content="Jun-19-03: WhatÕs downstream of Chr 2 near Hars2?">
<link rel=Stylesheet href="master03_stylesheet.css">
<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><script language=JavaScript><!--
-gId="slide0030.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:-.35%;left:2.51%;width:96.95%;height:11.66%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:16.66%;
left:1.36%;width:98.77%;height:66.66%'><span style='font-size:82%'><i>WhatÕs
downstream of Chr 2 near Hars2?</i></span><span style='font-size:82%;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<img border=0 src="slide0030_image115.gif" style='position:absolute;top:12.19%;
left:7.54%;width:61.58%;height:75.61%'>
<div class=O style='position:absolute;top:90.1%;left:5.16%;width:107.01%;
height:6.0%'><span style='font-family:"Gill Sans";font-size:233%;color:#E9EB5D'><i>modest
support that Actn2 is modulated by the Hars2 region</i></span></div>
</div>
<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>There is some support for
the hypothesis that Actn2 is downstream of a polymorphism in the Hars2
region. But again, due to the 10 to 20 Mb precision of the mapping data, this
relation could be generated by a large number of other polymorphisms close to
Hars2. In the absence of a biological connection between Actn2 and Hars2 we
have a weak hypothesis. If there were a plausible functional connection
between the two genes, then this hypothesis could be quickly upgraded.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=2>There is some support for
the hypothesis that Actn2 is downstream of a polymorphism in the Hars2
region. But again, due to the 10 to 20 Mb precision of the mapping data, this
relation could be generated by a large number of other polymorphisms close to
Hars2. In the absence of a biological connection between Actn2 and Hars2 we
have a weak hypothesis. If there were a plausible functional connection
between the two genes, then this hypothesis could be quickly upgraded.</font><br>
</td>
</tr>
</table>
</body>
</html>
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<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description
content="Jun-19-03: Does Hars2 correlate with Actn2 strongly?">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
<!--.sld
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width:6.0in !important;
height:4.5in !important;
font-size:76% !important;}
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</style>
<script language=JavaScript src=script.js></script><script language=JavaScript><!--
-gId="slide0031.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//-->
-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:-1.23%;left:2.51%;width:95.49%;height:9.01%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:13.72%;
left:1.38%;width:97.22%;height:76.47%'><span style='font-size:73%'><i>Does
Hars2 correlate with Actn2 strongly?</i></span><span style='font-size:82%;
mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<img border=0 src="slide0031_image116.gif" style='position:absolute;top:7.06%;
left:2.78%;width:47.15%;height:28.97%'><img border=0
src="slide0031_image117.gif" style='position:absolute;top:33.21%;left:30.06%;
width:67.41%;height:66.78%'><img border=0 src="slide0031_image118.gif"
style='position:absolute;top:17.49%;left:33.24%;width:15.36%;height:15.9%'>
<div class=O style='position:absolute;top:41.87%;left:2.64%;width:28.47%;
height:42.4%'><span style='position:absolute;top:0%;left:0%;width:94.41%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>Plenty of high </i></span></span><span
style='position:absolute;top:16.66%;left:0%;width:89.76%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>correlations, </i></span></span><span
style='position:absolute;top:33.75%;left:0%;width:89.76%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>including 2 </i></span></span><span
style='position:absolute;top:50.41%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>actins, but not
</i></span></span><span style='position:absolute;top:67.08%;left:0%;width:89.76%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>to Actn2 </i></span></span><span
style='position:absolute;top:83.75%;left:0%;width:89.76%'><span
style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>specifically.</i></span></span></div>
<div class=O style='position:absolute;top:16.43%;left:52.84%;width:25.03%;
height:6.89%'><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>Sort
by gene</i></span></div>
</div>
<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>We can test the Hars2 to
Actn2 connection directly. This process weakens the putative association. We
are ready to move on and examine other candidates in the Hars2 region near
D2Mit423.<span style="mso-spacerun: yes"> </span>Or in your case, please
start from the beginning using other genes and transcripts and tissues that
interest you more than this App-Hsp84-Hars2 example.</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>This concludes the first
demonstation of how to use some of the WebQTL features. Please explore.
Please also send feedback for improvements or additions to
rwilliam@nb.utmem.edu</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
</head>
<body bgcolor=black text=white>
<table 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=2>We can test the Hars2 to
Actn2 connection directly. This process weakens the putative association. We
are ready to move on and examine other candidates in the Hars2 region near
D2Mit423.<span style="mso-spacerun: yes"> </span>Or in your case, please
start from the beginning using other genes and transcripts and tissues that
interest you more than this App-Hsp84-Hars2 example.</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=2>This concludes the first
demonstation of how to use some of the WebQTL features. Please explore.
Please also send feedback for improvements or additions to
rwilliam@nb.utmem.edu</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0032.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0032.htm deleted file mode 100755 index 60a1bee2..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0032.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<link id=Main-File rel=Main-File href="WebQTLDemo.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description
content="Jun-19-03: Contact for comments and improvements:">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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-</script><script for=window event=onload language=JavaScript><!--
-if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//-->
-</script>
</head>
<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
onresize="_RSW()" onkeypress="_KPH(event)">
<div id=SlideObj class=sld style='position:absolute;top:0px;left:0px;
width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%);
visibility:hidden'><img src="master03_background.gif" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:2.29%;left:2.51%;width:94.7%;height:10.24%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:18.96%;
left:1.39%;width:97.2%;height:67.24%'><span style='font-size:73%'><i>Contact
for comments and improvements:</i></span><span style='font-size:82%;mso-special-format:
lastCR;display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:12.54%;left:6.62%;width:90.59%;height:32.68%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:" 0 ";position:absolute;top:0%;
left:1.46%;width:96.92%;height:100.0%'><span style='position:absolute;
top:0%;left:0%;width:100.0%'><span style='font-size:82%'>rwilliam@
nb.utmem.edu<br>
</span></span><span style='position:absolute;top:25.4%;
left:4.67%;width:95.47%'><span style='font-size:82%'>kenneth.manly@roswellpark.org<br>
</span></span><span
style='position:absolute;top:50.81%;left:4.67%;width:95.47%'><span
style='font-size:82%'>lulu@ nb.utmem.edu<br>
</span></span><span
style='position:absolute;top:75.67%;left:4.67%;width:95.47%'><span
style='font-size:82%'>echesler@ nb.utmem.edu</span></span></div>
</div>
</div>
<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>END</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
-function playList() { - -} -//-->
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<head>
<meta name=ProgId content=PowerPoint.Slide>
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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<body bgcolor=black text=white>
<table border=0 width="100%">
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<td width="100%"></td>
</tr>
<tr>
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<td align=left colspan=1><font face=Verdana size=2>END</font><br>
</td>
</tr>
</table>
</body>
</html>
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genomics</title>
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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content="Jun-19-03: WebQTL Demonstration One please link to www.webqtl.org/search.html">
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One<br>
</i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0.03 * g_width; myheight = 0.06 * g_height; mywidth = 0.89 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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</i></span></span></layer></div>
</layer></div>
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<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.63 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='mso-special-format:nobullet;display:none;
color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 1: How to discover
shared </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'>2Ð14)<br>
</span></span></layer></div>
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56'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.6 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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upstream </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'>modulators (15Ð25)<br>
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56'><script> - mytop = 0 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.66 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute;
left:-7.6%;font-family:Times;font-size:99%'>3.</span></span><span
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targets</span></span></layer></div>
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<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%;
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17'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span
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display:none'><br>
</span></div>
</layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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mso-special-format:lastCR;display:none'><br>
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%;
color:#E9EB5D;mso-color-index:3'><i>PowerPoint ÒNormal viewÓ has notes that </i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.78 * g_width; - 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:250%;
color:#E9EB5D;mso-color-index:3'><i>may be useful companions to these slides.</i></span><span
style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index:
3;mso-special-format:lastCR;display:none'><br>
</span></span></layer></div>
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<td align=left colspan=1><font face=Helvetica size=3>Welcome to a short
demonstation of WebQTL. Please adjust the wize of windows on your monitor so
that you can see part of this page as well as WebQTL windows. WebQTL will
produce a potentially large number of new windows (pop-ups), so you may need
to modify your browser preferences to permit pop-ups.<span
style="mso-spacerun: yes"> </span>In this demonstration, we
explore one important transcript expressed in the brain: the amyloid beta
precursor protein messenger RNA. The product of this mRNA, the APP protein,
is associated with Alzheimer disease.</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=Helvetica size=3>(Initial version of
June 2003 by Rob Williams, Last edits June 16, 2003 by RW.)</font><br>
</td>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>or
webqtl.org/search.html (mirror)</span></div>
</layer></div>
</layer><script> - mytop = 0.16 * g_height; myleft = 0.02 * g_width; myheight = 0.81 * g_height; mywidth = 0.71 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
mso-color-index:3'>enter<br>
</span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.21 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
mso-color-index:3'><i>amyloid beta</i></span><span style='font-family:"Gill Sans";
font-size:250%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><i><br>
</i></span></div>
</layer></div>
</layer><script> - mytop = 0.78 * g_height; myleft = 0.79 * g_width; myheight = 0.11 * g_height; mywidth = 0.11 * g_width; - 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%;
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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<div>
<layer>
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<layer>
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<layer>
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<layer>
<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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348;mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:348;
mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display:none;
color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>link to
www.webqtl.org/search.html</span></div>
</layer></div>
</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=Helvetica size=3>WebQTL can be used to
enter your own trait data or to work with data that we have entered for you.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Linking to
http://www.webqtl.org/search.html will get you a version of the window
above. It may not be identical in layout but it will have the key features.
Please follow the intructions on the slide. Of course, we encourage you to
enter your own terms of interest.</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=Helvetica size=3>Two points: If you make
a search term too complex you may get no hits. if you make it too simple
(for example, APP) then you may get too much. Experiment.</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=Helvetica size=3>If you just link to</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>http://www.webqtl.org
you will NOT see the window above but will see text that will help you to
enter your own data.<span style="mso-spacerun: yes"> </span>To get to
a version of the window shown above you will need to click on the phrase<span
style="mso-spacerun: yes"> </span>RNA expression and Phenotype
Databases in the upper banner.</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=Helvetica size=3>If you do not get a new
page within 30 seconds then there is<span style="mso-spacerun: yes">
</span>a problem: try the mirror site http://webqtl.org/search.html.</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 diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0035.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0035.htm deleted file mode 100755 index c53c9bbc..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0035.htm +++ /dev/null @@ -1,116 +0,0 @@ -<html>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%;
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
mso-color-index:3'><i>amyloid beta<br>
</i></span></div>
</layer><script> - mytop = 0.11 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
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font-size:250%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = -0.04 * g_height; myleft = 0.07 * g_width; myheight = 0.18 * g_height; mywidth = 0.84 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.04 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 0.82 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%;
mso-text-raise:0%'><span style='font-size:91%'>Search results</span><span
style='mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</LAYER>
-
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<div id=NotesObj style='display:none'>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>If all goes well, you
will see a version of this window. WebQTL will display up to about 100 hits.
If a search generates larger numbers of hits then you will need to refine
your search terms.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0036.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0036.htm deleted file mode 100755 index ae7843aa..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0036.htm +++ /dev/null @@ -1,122 +0,0 @@ -<html>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
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genomics</title>
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mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none;
color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>First page of data: The
ÒTrait Data FormÓ</span></div>
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<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%;
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<div><span style='font-size:200%;color:#E9EB5D'><i>Click here<br>
</i></span></div>
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<div><span style='font-size:200%;color:#E9EB5D'><i>to learn<br>
</i></span></div>
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<div><span style='font-size:200%;color:#E9EB5D'><i>about<br>
</i></span></div>
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<div><span style='font-size:200%;color:#E9EB5D'><i>data<br>
</i></span></div>
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<div><span style='font-size:200%;color:#E9EB5D'><i>source</i></span></div>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>The Trait Data and
Editing Form is the single more important page from the point of view of
working with WebQTL data. Please read the text carefully. Explore the links,
but do not close this page. We will need it many more times in this
demonstration.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
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-</script>
</body>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm deleted file mode 100755 index bb776db5..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html>
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mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none;
color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Data sources: Phenotpyes
and genotypes</span></div>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>There are already five
databases in WebQTL. Each will eventually have a page like this describing
the data source and appropriate citations to these databases. The great
majority of data in WebQTL were generated in our own labs and those of our
collaborators.<span style="mso-spacerun: yes"> </span>We welcome you
to use these data, but caution you that there are inevitably lots of little
problems and issues that may compromise some results. Be cautious and
skeptical. Ask us questions before you leap to publication. And please, if
you find the data useful or can verify or refute data, LET US KNOW. We would
like to add you to our reference section and add links to improvements.</font><br>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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<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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.09 * g_width; - 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:217%;
color:#E9EB5D;mso-color-index:3'>Trait data for each strain with SE when known.
For array data </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.08 * g_width; - 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:217%;
color:#E9EB5D;mso-color-index:3'>the scale is ~ log base 2.<span
style="mso-spacerun: yes"> </span></span><span style='font-size:
183%;color:#E9EB5D;mso-color-index:3'>F1=13.752 = 2^13.752 = 13796 </span><span
style='font-family:"Gill Sans";font-size:183%;color:#E9EB5D;mso-color-index:
3;mso-special-format:lastCR;display:none'><br>
</span></span></layer></div>
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<div id=NotesObj style='display:none'>
<table style='color:white' border=0 width="100%">
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<td width="100%"></td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>This<span
style="mso-spacerun: yes"> </span>slide shows you the<span
style="mso-spacerun: yes"> </span>lower parts of the Trait Data Page.
We expect to make many small modification of this page, so do not be
surprised if some elements have been moved around.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm deleted file mode 100755 index 0b96295c..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm +++ /dev/null @@ -1,104 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href=WebQTLDemo.ppt>
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Discovering shared
expression patterns</span></div>
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<td align=left colspan=1><font face=Helvetica size=3>Finally, we can now
start an analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>We ask a simple
question:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Do differences in App
transcript expression correlate with those of any other transcripts in the
forebrain?</font><br>
</td>
</tr>
</table>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>The </span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript neighborhood</span></div>
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<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%;
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style='text-align:left'><span style='font-size:150%;color:#E9EB5D;mso-color-index:
3'><b>Question: </b></span><span style='font-size:133%;color:#E9EB5D;
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style='text-align:left'><span style='font-size:133%;color:#E9EB5D;mso-color-index:
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style='text-align:left'><span style='font-size:133%;color:#E9EB5D;mso-color-index:
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-
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<div id=NotesObj style='display:none'>
<table style='color:white' border=0 width="100%">
<tr>
<td width=5 nowrap></td>
<td width="100%"></td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>The answer is a strong
Yes. A very large number of transcripts have correlations above 0.7
(absolute value) with App mRNA. The precise number today is 208. But this
will change as we add more strains and arrays. In any case, this is a fairly
large number and all of these correlations are significant at alpha .05 even
when correcting for the enormous numbers<span style="mso-spacerun:
yes"> </span>of tests (12422 tests).</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=Helvetica size=3>What does this imply?</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=Helvetica size=3>That there can be
massive codependence of expression variance among transcripts. App is NOT an
isolated instance. This is improtant biologically and statistically. From a
statistical perspective, we would like to know how many ÒindependentÓ test
we effectively are performing when we use array data in this way. Are we
testing 12000 independent transcripts or just 1200 transcriptional ÒmodulesÓ
each with blurred boarders but each with about 10 effective members. There
is no answer yet, but we probaby have a large enough data set to begin to
answer this question.</font><br>
</td>
</tr>
</table>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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neighborhood</span></div>
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<td width=5 nowrap></td>
<td width="100%"></td>
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<tr>
<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"> </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>
<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=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>
</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=Helvetica size=3>What are all of
the<span style="mso-spacerun: yes"> </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"> </span>ÒatÓ. 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"> </span>If there is no star symbol, then it
is not even formally ÒsuggestiveÓ but does make an interesting looking blip
on the QTL radar screen.</font><br>
</td>
</tr>
</table>
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style='text-align:left'><span style='mso-special-format:nobullet;display:none;
color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>What a network is likely
to look like (but </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:
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style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>will not be center of universe).</span></span></layer></div>
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<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%'><span style='font-size:133%;color:#FF0F0F'><b><i>App</i></b></span></div>
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<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>What networks are
likely to really look like. This slide is taken from Lumeta Inc.<span
style="mso-spacerun: yes"> </span>(www.lumeta.com). It actually
illustrates the structure of connections across the<span
style="mso-spacerun: yes"> </span>Internet. The large green area is a
major Internet provider (WorldCom before the fall?).<span
style="mso-spacerun: yes"> </span>Check<span style="mso-spacerun:
yes"> </span>out Lumeta to see some more lovely graphs of this sort.
Most biologists are familiar with simple sketches, but this is what we will
have to be prepared to contend with soon.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
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-</script>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0043.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0043.htm deleted file mode 100755 index e0be795e..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0043.htm +++ /dev/null @@ -1,112 +0,0 @@ -<html>
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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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style='text-align:left'><span style='font-size:68%'><i>Are there experimental
results to corroborate a link </i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:68%'><i>between App with
Hsp84-1?</i></span></span></layer></div>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%;
color:#E9EB5D'><i>Yes: Heat shock 84-1 induces the expression of App, </i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.84 * g_width; - 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:250%;
color:#E9EB5D'><i>ubiquitin, and pyruvate kinase</i></span></span></layer></div>
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:250%;
color:#E9EB5D'><i>Having ÒconfirmedÓ these known relations, we can </i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; - 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:250%;
color:#E9EB5D'><i>now add new members to this family: Atp6l, Gnas, </i></span></span></layer><script> - mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.84 * g_width; - 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:250%;
color:#E9EB5D'><i>Ndr4. A thin veneer of functional genomics.</i></span></span></layer></div>
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</LAYER>
-
<layer>
<div id=NotesObj style='display:none'>
<table style='color:white' border=0 width="100%">
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<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Having worked with
WebQTL now for 30 minutes, do we know anything new? The hypothesis that we
have generated (but not validated) is that three transcripts: Atp6l, Gnas,
and Ndr4 are part of a family of genes that are coregulated in normal mouse
forebrain with App and Hsp84-1. We need to add functional and mechanistic
significance to this hypothesis to make it biologically vibrant. But from a
statiistical standpoint it is a strong inference.</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=Helvetica size=3>Please donÕt say: But
these are mere correlations. A high correlation in this context has a
biological basis. The real question is are we smart enough to understand the
web (not chain) of causality that produced the correlation. Once we
understand the web of causality, does it have utility? Very often the answer
will be NO. This will often be the case when a high correlation is generated
by linkage disequilibrium of sets of polymorphisms that modulate a set of
mechanistically separated traits. Chromosomal linkage can produce
correlations that are not mechanistic in the conventional sense used by
molecular biologists. For example, clusters<span style="mso-spacerun:
yes"> </span>of hox transcription factor genes tend to be close
physically to keratin gene clusters, and one might expect shared patterns of
variance produced by this linkage in a mapping panel, no matter how large.</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=Helvetica size=3>If Affymetrix designed
probe sets with reasonable care, if we did the experiments correctly, if we
sampled animals appropriately, then a correlation of 0.70 or higher between
transcripts in the brain tells you that these two transcripts are
effectively coupled in this set of animals under this set of conditions.
More than 50% the variance in the expression of one transcript can be
predicted from the other. That is a major piece of information that could be
of significant clinical, economic, and predictive value, whatever its
causes. Yes, correlation coefficients are noisy and have large error terms,
but we have larger n of strains coming to the rescue. Expect more than 50
BXD lines soon.</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=Helvetica size=3>This is a thin veneer
of functional genomics. It is enough to generate some marvelous hypotheses
in a semi-automated way.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0044.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0044.htm deleted file mode 100755 index 06443316..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0044.htm +++ /dev/null @@ -1,107 +0,0 @@ -<html>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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<div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans";
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>2.45 billion scatter
plots: </span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>here
is one of the best</span></div>
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mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:283%;
color:#003399;mso-color-index:4'><i>App</i></span><span style='font-family:
"Gill Sans";font-size:283%;color:#E9EB5D;mso-color-index:3;mso-special-format:
lastCR;display:none'><i><br>
</i></span></div>
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<table style='color:white' border=0 width="100%">
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<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>The correlation between
App and heat shock protein 84-1 transcript is most impressive.<span
style="mso-spacerun: yes"> </span>Since WebQTL now contains total of
about 70,000 traits in the BXD strains, we could produce as many as to 70k x
35k scatter plots of this type. Since all of the<span style="mso-spacerun:
yes"> </span>correlations come for a common reference population,
none<span style="mso-spacerun: yes"> </span>of the correlations are
blantantly silly. However the great majority may be uninterpretable and a
very large number may be meaningless given the signal-to-noise ratios of
some measurements. With about 30 strains, correlations above 0.7 have a
reasonably low false positive rate.</font><br>
</td>
</tr>
</table>
</div>
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<td align=left colspan=1><font face=Helvetica size=3>We can compare App
expression inthe forebrain against transcript expression in hematopoietic
stem cells. Some of these correlations are significant, but it may be
difficult to discovery of shared genetic (linkage disequilibrium) or
molecular processes that give rise to these correlation.</font><br>
</td>
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<td align=left colspan=1><br>
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<td align=left colspan=1><font face=Helvetica size=3>The GNF Hematopoietic
stem cell data belong to Gerald de Haan (University of Groningen) and
Michael Cooke (Genomics Institute of the Novartis Research Foundation).</font><br>
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<td align=left colspan=1><font face=Helvetica size=3>Another example, but in
this case we are generating correlations between variation in transcript
levels with a database of approximately 430 published (and unpublished)
phenotypes from BXD strains. Notice that the N of strains is variable (from
21 to 28 above). Rank order statistics is more appropriate when N is under
30.</font><br>
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<td align=left colspan=1><font face=Helvetica size=3>The Published
Phenotypes database was prepared by Elissa Chesler and Robert Williams from
data extracted from the literature or sent to us for inclusion by our
colleagues. We especially thank John Crabbe (Oregon HSU) and Byron Jones
(Pennsylvania SU) for providing us with large pre-compiled data tables.</font><br>
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</i></span></span></layer></div>
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3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute;
left:-8.06%;font-family:Times;font-size:99%'>1.</span></span><span
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expression </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute;
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3'>modulators (QTLs)<br>
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targets</span></span></layer></div>
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display:none'><br>
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<td align=left colspan=1><font face=Helvetica size=3>Part 2: Mapping
upstream modulators or QTLs. A quantitative trait locus is a chromosomal
region that harbors one or a few polymorphic gene loci that influence a
trait. We are going to be looking for QTLs that modulate the steady state
expression level of App in the adult mouse forebrain.</font><br>
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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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F1<br>
</b></span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:
lastCR;display:none'><b><br>
</b></span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.39 * g_height; myleft = 0.22 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.22 * g_width; -yy = 0.39 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image034.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.39 * g_height; myleft = 0.38 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.38 * g_width; -yy = 0.39 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image035.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.39 * g_height; myleft = 0.55 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.55 * g_width; -yy = 0.39 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image036.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.39 * g_height; myleft = 0.72 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.72 * g_width; -yy = 0.39 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image037.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.43 * g_height; myleft = 0.43 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.43 * g_width; -yy = 0.43 * g_height; -ht = 0.03 * g_height; -wd = 0.11 * g_width; -document.write( -'<img border=0 src="slide0016_image038.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.6 * g_height; myleft = 0.2 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.2 * g_width; -yy = 0.6 * g_height; -ht = 0.03 * g_height; -wd = 0.09 * g_width; -document.write( -'<img border=0 src="slide0016_image039.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.71 * g_height; myleft = 0.58 * g_width; myheight = 0.27 * g_height; mywidth = 0.2 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.03 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 0.17 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-family:Arial;font-size:117%;
color:#FFFF99'><b>20 generations </b></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-family:Arial;font-size:117%;
color:#FFFF99'><b>brother-sister </b></span></span></layer><script> - mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-family:Arial;font-size:117%;
color:#FFFF99'><b>matings</b></span><span style='font-family:Arial;font-size:
233%;color:#FFFF99;display:none'><b><br>
</b></span></span></layer></div>
</layer><script> - mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17'><span style='font-family:Arial;font-size:233%;
color:#FFFF99;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.6 * g_height; myleft = 0.5 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.5 * g_width; -yy = 0.6 * g_height; -ht = 0.03 * g_height; -wd = 0.09 * g_width; -document.write( -'<img border=0 src="slide0016_image040.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.62 * g_height; myleft = 0.54 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.54 * g_width; -yy = 0.62 * g_height; -ht = 0.28 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image041.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.61 * g_height; myleft = 0.79 * g_width; myheight = 0.03 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.79 * g_width; -yy = 0.61 * g_height; -ht = 0.03 * g_height; -wd = 0.1 * g_width; -document.write( -'<img border=0 src="slide0016_image042.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.62 * g_height; myleft = 0.83 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.83 * g_width; -yy = 0.62 * g_height; -ht = 0.28 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image043.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.92 * g_height; myleft = 0.21 * g_width; myheight = 0.1 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD1</span><span
style='font-family:Arial;font-size:150%;color:#484848;display:none'><br>
</span></div>
</layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#484848;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.92 * g_height; myleft = 0.51 * g_width; myheight = 0.1 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD2<br>
</span></div>
</layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.92 * g_height; myleft = 0.8 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - 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%;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>BXD80</span></div>
</layer></div>
</layer><script> - mytop = 0.9 * g_height; myleft = 0.64 * g_width; myheight = 0.17 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.15 * g_height; mywidth = 0.16 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.16 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:300%;color:#FFFF99'>+ É +<br>
</span></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:300%;color:#FFFF99;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.62 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.04 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F2<br>
</b></span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:
lastCR;display:none'><b><br>
</b></span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.54 * g_height; myleft = 0.18 * g_width; myheight = 0.01 * g_height; mywidth = 0.75 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.18 * g_width; -yy = 0.54 * g_height; -ht = 0.01 * g_height; -wd = 0.75 * g_width; -document.write( -'<img border=0 src="slide0016_image044.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.54 * g_height; myleft = 0.17 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.17 * g_width; -yy = 0.54 * g_height; -ht = 0.03 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0016_image045.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.54 * g_height; myleft = 0.32 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.32 * g_width; -yy = 0.54 * g_height; -ht = 0.03 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0016_image046.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.54 * g_height; myleft = 0.48 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.48 * g_width; -yy = 0.54 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0016_image047.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.54 * g_height; myleft = 0.62 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.62 * g_width; -yy = 0.54 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0016_image048.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.54 * g_height; myleft = 0.77 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.77 * g_width; -yy = 0.54 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0016_image049.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.54 * g_height; myleft = 0.92 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.92 * g_width; -yy = 0.54 * g_height; -ht = 0.03 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0016_image050.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.44 * g_height; myleft = 0.49 * g_width; myheight = 0.1 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.49 * g_width; -yy = 0.44 * g_height; -ht = 0.1 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0016_image051.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.57 * g_height; myleft = 0.15 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.15 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image052.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.57 * g_height; myleft = 0.3 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.3 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image053.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.57 * g_height; myleft = 0.46 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.46 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image054.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.57 * g_height; myleft = 0.6 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.6 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image055.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.75 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image056.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.57 * g_height; myleft = 0.9 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.9 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0016_image057.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.84 * g_height; myleft = 0.56 * g_width; myheight = 0.01 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.56 * g_width; -yy = 0.84 * g_height; -ht = 0.01 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0016_image058.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.8 * g_height; myleft = 0.25 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.25 * g_width; -yy = 0.8 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0016_image059.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.84 * g_height; myleft = 0.86 * g_width; myheight = 0.02 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.86 * g_width; -yy = 0.84 * g_height; -ht = 0.02 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0016_image060.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.75 * g_height; myleft = 0.01 * g_width; myheight = 0.14 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.13 * g_width; - 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> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'><b>BXD RI<br>
</b></span></div>
</layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'><b>Strain set<br>
</b></span></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.12 * g_height; myleft = 0.14 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.14 * g_width; -yy = 0.12 * g_height; -ht = 0.06 * g_height; -wd = 0.1 * g_width; -document.write( -'<img border=0 src="slide0016_image061.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.1 * g_height; myleft = 0.76 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.76 * g_width; -yy = 0.1 * g_height; -ht = 0.08 * g_height; -wd = 0.14 * g_width; -document.write( -'<img border=0 src="slide0016_image062.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.2 * g_height; myleft = 0.17 * g_width; myheight = 0.14 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.08 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>fully<br>
</span></div>
</layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>inbred<br>
</span></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99;mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.38 * g_height; myleft = 0.02 * g_width; myheight = 0.1 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>isogenic<br>
</span></div>
</layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99;mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.54 * g_height; myleft = 0.01 * g_width; myheight = 0.14 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.11 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>hetero-<br>
</span></div>
</layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>geneous<br>
</span></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99;mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.74 * g_height; myleft = 0.29 * g_width; myheight = 0.22 * g_height; mywidth = 0.22 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.19 * g_height; mywidth = 0.19 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>Recombined </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>chromosomes </span></span></layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>are needed for </span></span></layer><script> - mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-family:Arial;font-size:150%;
color:#FFFF99'>mapping<br>
</span></span></layer></div>
</layer><script> - mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%;
color:#FFFF99;mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.1 * g_height; myleft = 0.25 * g_width; myheight = 0.1 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.09 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>female<br>
</span></div>
</layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.1 * g_height; myleft = 0.64 * g_width; myheight = 0.1 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.06 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>male<br>
</span></div>
</layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.05 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
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<td align=left colspan=1><font face=Verdana size=3>The next set of slides
provide a very short interlude on QTL mapping. You will need to do some
independent reading on this topic if this is your first exposure to QTL
mapping. The recombinant inbred strains that we are using in WebQTL and in
this particular demo were generated about 25 years ago by Dr. Ben Taylor at
The Jackson Laboratory. He crossed a female C57BL/6J mouse with a male
DBA/2J mice. At the bottom of this slide we have schematized one chromosome
pair from three out of 80 BXD RI strains.<span style="mso-spacerun:
yes"> </span>The dashed vertical lines that lead to the final BXD RI
lines involve 20 full sib matings (about 6 years of breeding). Some lines
die<span style="mso-spacerun: yes"> </span>out during inbreeding. For
example, there is no extant BXD3 or BXD4 strain.</font><br>
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</layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.21 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.43 * g_height; myleft = 0.71 * g_width; myheight = 0.19 * g_height; mywidth = 0.25 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.24 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.24 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-size:267%;color:#F6BF69'>B6 strain</span><span
style='font-family:Palatino;font-size:333%;color:#F6BF69;display:none'><br>
</span></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.21 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-family:Palatino;font-size:333%;color:#F6BF69;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.17 * g_height; myleft = 0.31 * g_width; myheight = 0.42 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.31 * g_width; -yy = 0.17 * g_height; -ht = 0.42 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0017_image076.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.4 * g_height; myleft = 0.31 * g_width; myheight = 0.03 * g_height; mywidth = 0.39 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.31 * g_width; -yy = 0.4 * g_height; -ht = 0.03 * g_height; -wd = 0.39 * g_width; -document.write( -'<img border=0 src="slide0017_image077.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.17 * g_height; myleft = 0.4 * g_width; myheight = 0.31 * g_height; mywidth = 0.3 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.03 * g_height; myleft = 0.01 * g_width; myheight = 0.26 * g_height; mywidth = 0.27 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.27 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.27 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>amount of
</i></span></span></layer><script> - mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.27 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>transcript</i></span><span
style='font-family:Palatino;font-size:367%;color:#E9EB5D;display:none'><br>
</span></span></layer></div>
</layer><script> - mytop = 0.17 * g_height; myleft = 0 * g_width; myheight = 0.09 * g_height; mywidth = 0.27 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.06 * g_height; myleft = 0.72 * g_width; myheight = 0.19 * g_height; mywidth = 0.21 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.18 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-size:267%;color:white'>4 </span><span style='font-size:
233%;color:white'>units</span><span style='font-family:Palatino;font-size:333%;
color:#E9EB5D;display:none'><br>
</span></div>
</layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.29 * g_height; myleft = 0.72 * g_width; myheight = 0.19 * g_height; mywidth = 0.21 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.18 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-size:267%;color:white'>2</span><span style='font-size:
233%;color:white'> units</span><span style='font-family:Palatino;font-size:
333%;color:#E9EB5D;display:none'><br>
</span></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.15 * g_height; myleft = 0.31 * g_width; myheight = 0.05 * g_height; mywidth = 0.4 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.31 * g_width; -yy = 0.15 * g_height; -ht = 0.05 * g_height; -wd = 0.4 * g_width; -document.write( -'<img border=0 src="slide0017_image078.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.17 * g_height; myleft = 0.09 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:300%;color:#E2EBF0'>D<br>
</span></div>
</layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.17 * g_height; myleft = 0.17 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:300%;color:#F6BF69'>B<br>
</span></div>
</layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.77 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.02 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 1.03 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * g_height; mywidth = 1.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:233%;color:#E2EBF0'>D</span><span
style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%;
color:#E9EB5D'>and </span><span style='font-size:233%;color:#F6BF69'>B</span><span
style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%;
color:#E9EB5D'>may be SNP-like variants in the promoter </span></span></layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:200%;color:#E9EB5D'>itself (cis
QTL) or in </span><span style='font-size:200%;color:#EAEC5E'>upstream genes
(trans QTLs)</span><span style='font-size:300%;color:#E9EB5D;display:none'><br>
</span></span></layer></div>
</layer><script> - mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.89 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:300%;color:#E9EB5D;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0.04 * g_width; myheight = 0.16 * g_height; mywidth = 0.22 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>UPSTREAM<br>
</span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>modulators<br>
</span></div>
</layer><script> - mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.05 * g_height; mywidth = 0.2 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:" 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0.44 * g_width; myheight = 0.18 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.14 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-size:300%;color:#E2EBF0'>High<br>
</span></div>
</layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.63 * g_height; myleft = 0.08 * g_width; myheight = 0.18 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:300%;color:#E2EBF0'>D<br>
</span></div>
</layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.63 * g_height; myleft = 0.15 * g_width; myheight = 0.18 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; - 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%;
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<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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display:none'><br>
</span></div>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%;
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17;mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:17'><span
style='font-family:Gadget;font-size:167%;color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2
- etc-3'UTR >>>>></span></div>
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<div style='mso-line-spacing:" 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:200%;color:#E9EB5D'><i>trans QTL</i></span><span
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<td width="100%"></td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>This slide is
illustrates two categories of QTLs that modulate variability in transcript
abundance.</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=Helvetica size=3>1. cis QTLs are defined
as QTLs that are closely linked to the gene whose transcript is the measured
trait. For example, a polymorphism in the promoter that affects the binding
of a transcription factor. However, cis QTLs can be far upstream or
downstream polymorphisms in enhancers. They may also be polymorphisms in
neigghboring genes.</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=Helvetica size=3>2. trans QTLs map far
enough away from the location of the gene that gives rise to the transcript
that is being measured so that we can be quite certain that the QTL is not
IN the gene itself. The most blatant type of trans-QTL would be a
polymorphism in a transcription factor. BUT in the majority of cases, the
trans QTLs can be far removed in a mechanistic sense from the actual events
modulating transcript abundance. That is why there are three overlappoing
arrows above.<span style="mso-spacerun: yes"> </span>The way in which
an upstream polymorphism influences a downstream difference in mRNA
abundance can be very indirect. Effects can :</font><br>
</td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3><span
style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun:
yes"> </span>cross tissue types (a polymorphic liver enzyme may affect
CNS gene expression)</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3><span
style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun:
yes"> </span>cross time (the modulator is only expressed for one day
during development but has permanent effects in adults),</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3><span
style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun:
yes"> </span>may be contingent on environmental factors (heat shock
may trigger the expression of a polymorphic factor that affects mRNA
abundance).</font><br>
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mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span
style='font-family:Verdana;font-size:73%'><i>WebQTL to exploring upstream
control</i></span></div>
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<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%'><span style='font-family:"Gill Sans";font-size:217%;
color:#FF0F0F'>Just click</span></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>Back to the demo. Please
bring the Traiit Data and Editing window to the front and look for the
Interval Mapping button. Please confirm that you are back to the trait
amyloid beta precursor protein.<span style="mso-spacerun: yes">
</span>If so, then just click the button.</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>Notice that the default
for:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes)
is ALL</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Select Probes is Probe
Set</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Options: Permuation test
YES<span style="mso-spacerun: yes"> </span>(1000 is the default
number)</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test
YES (1000 is the default number)</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 diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0051.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0051.htm deleted file mode 100755 index 39d20b2b..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0051.htm +++ /dev/null @@ -1,127 +0,0 @@ -<html>
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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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to exploring upstream control.</i></span></div>
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<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%'><span style='font-size:233%;color:#E9EB5D'><i>App maps on
Chr 16 here</i></span></div>
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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%;
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<div><span style='font-size:267%;color:#E9EB5D'><i>Is App modulated by Chr
2?<br>
</i></span></div>
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<div><span style='font-size:267%;color:#E9EB5D'><i>Probably, but donÕt bet the
farm. </i></span></div>
</layer></div>
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</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>This is the main output
type: a so-called full genome interval map.</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 X-axis represents all
19 autosomes and the X chromosome as if they were laid end to end with short
gaps between the telomere of one chromosome and the centromere of the next
chromosome (mouse chromsomes only have a single long arm and the centromere represents
the origin of each chromosome for numerical purpose: 0 centimorgans and
almost 0 megabases). The blue labels along the bottom of the figure list a
subset of markers that were used in mapping. We used 753 markers to perform
the mapping but here we just list five markers per chromosome.</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 thick blue wavy line
running across chromsomes summarizes the strength of association between
variation in the phenotype (App expression differences) and the two
genotypes of 753 markers and the intervals between markers (hence, interval
mapping).<span style="mso-spacerun: yes"> </span>The height of the
wave (blue Y-axis to the left) provides the likelihood ratio statistic
(LRS). Divide by 4.61 to convert these values to LOD scores.<span
style="mso-spacerun: yes"> </span>Or you can read them as a
chi-square-like statistic.</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 red line and the red
axis to the far right provides an estimate of the effect<span
style="mso-spacerun: yes"> </span>that a QTL has on expression of App
(this estimate of the addtive effect tends to be an overestimate). If the
red line is below the X-axis then this means that the allele inherited from
C57BL/6J (B6 or B) at a particular marker is associated with higher values.
If the red line is above the X-axis then the DBA/2J allele (D2 or D) is
associated with higher traits. Multiply the additive effect size by 2 to
estimate the difference between the set of strains that have the B/B
genotype and the D/D genotype at a specific marker. For example, on Chr 2
the red line<span style="mso-spacerun: yes"> </span>peaks at a value<span
style="mso-spacerun: yes"> </span>of about 0.25. That means that this
region of chromosome 2 is responsible for a 0.5 unit expression difference
between B/B strains and the D/D strains. Since the units are log base 2,
this is 2^0.5, or about a 41% difference in expression with the D/D group
being high.</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 yellow histogram
bars: These summarize the results of a whole-genome bootstrap of the trait
that is performed 1000 times. What is a bootstrap? A bootstrap provides you
a metho of evaluating whether results are robust. If we drop out one strain,
do we still get the same results? When mapping quantitative traits, each
strain normally gets one equally weighted vote. But inthe bootstrap
procedure, we give each strain a random weighting factor of between 0 and
1.<span style="mso-spacerun: yes"> </span>We then remap the trait and
find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this
example, most bootstrap results cluster on Chr 2 under the LRS peak. That is
somewhat reassuring. But notice that a substantial number of bootstrap
results prefer Chr 7 or Chr 18.</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 horizontal dashed
lines at 9.6 and 15.9. These lines are the LRS values associated with the
suggestive and significant false positive rates for genome-wide scans
established by permuations of phenotypes across genotypes. We shuffle
randomly 1000 times and obtain a distribution of peak LRS scores to generate
a null distribution. Five percent of the time, one of these permuted data
sets will have a peak LRS higher than 15.9. We call that level the 0.05
significance threshold for a whole genome scan. The p = 0.67 point is the
the suggestive level, and corresponds to the green dashed line.<span
style="mso-spacerun: yes"> </span>These thresholds are conservative
for transcripts that have expression variation that is highly heritable. The
putative or suggestive QTL on Chr 2 is probably more than just suggestive.</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>One other point: the
mapping procedure we use is computationally very fast, but it is relatively
simple. We are not looking for gene-gene interactions and we are not fitting
multiple QTLs in combinations.<span style="mso-spacerun: yes">
</span>Consider this QTL analysis a first pass that will highlight hot spots
and warm spots that are worth following up on using more sophisticated
models.</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>CLICKABLE REGIONS:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>1. If you click on the
Chromosome number then you will generate a new map just for that chromosome.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. If you click on the
body of the map, say on the blue line, then you will generate a view<span
style="mso-spacerun: yes"> </span>on a 10 Mb window of that part of
the genome from the UCSC Genome Browser web site.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. If you click on a
marker symbol, then you will generate a new Trait data and editing window
with the genotypes loaded into the window just like any other trait. More on
this later.</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>NOTE: you can drag these
maps off of the browser window and onto your desktop. The will be saved as
PNG or PDF files. You can import them into Photoshop or other programs.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
-</script><script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0052.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0052.htm deleted file mode 100755 index 54843d1c..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0052.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html>
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modulated!</i></span></div>
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<tr>
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<td align=left colspan=1><font face=Verdana size=3>App has a suggestive QTL
on Chr 2. What about the neighbors that we defined as having shared
expression patterns. This figure shows that members of the immediate App
neigborhood share a weak Chr 2 QTL.<span style="mso-spacerun: yes">
</span>That is what the blue oval in the background is meant to represent.
But some transcripts, such as Ndr4 and Psen2 do not share this Chr 2
interval.</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>QUESTION: What kind of
headway can we make in detemining what polymorphism or polymorphisms on Chr
2 near 130 Mb might contribute to the variance in the expression of all of
these important transcripts?</font><br>
</td>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0053.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0053.htm deleted file mode 100755 index baaa7eee..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0053.htm +++ /dev/null @@ -1,139 +0,0 @@ -<html>
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style='font-family:Verdana;font-size:73%'><i>Which gene is the QTL?</i></span></div>
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<div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>Right
<br>
</i></span></div>
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<div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>&<br>
</i></span></div>
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<div style='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i>candidates</i></span></div>
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<td align=left colspan=1><font face="Times New Roman" size=4><b>Candidate
Genes: </b><span style="mso-spacerun: yes"> </span>The best we can do
at this point is to make an educated guess about the candidacy status of all
genes in the QTL support interval. For sake of argument, lets say that we
are confident that the polymorphism is located between 130 and 150 Mb (20
Mb, equivalent to roughly 10 cM). There will typically be 12 to 15 genes per
Mb, so we now would like to evaluate 240 to 300 positional candidates. We
would like to highlight the biologically relevant subset of candidates. We
could look through gene ontologies and expression levels to help us winnow
the list. An alternate way avaiable using WebQTL is to generate a list of
those genes in this 20 Mb interval that have transcripts that co-vary in
expression with App expression.</font><br>
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<tr>
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<td align=left colspan=1><br>
</td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>To do this, go
back to the Trait Data and Editing window. Sort the correlations by
position. Select Return = 500. Then scroll down the list to see positional
candidates that share expression with App.</font><br>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>There are
several candidates that have high correlation with App even in this short 20
Mb interval. We can rank them by correlation, but they are all close.<span
style="mso-spacerun: yes"> </span>There is one other imporant approach
to ranking these candidates. Are they likely to contain polymorphisms? We
can assess the likelihood that they contain polymorphisms by mapping each
transcript to see if any have strong cis QTLs. The logic of this search is
that a transcript that has a strong cis-QTL is likely to contain functional
polymorphisms that effect its own expression. This make is more like that
the transcript is a ÒcausativeÓ factor since it is likely to be polymorphic.</font><br>
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<td align=left colspan=1><br>
</td>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0054.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0054.htm deleted file mode 100755 index 1e0d7468..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0054.htm +++ /dev/null @@ -1,125 +0,0 @@ -<html>
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<div><span style='font-size:200%;color:#E9EB5D'><i>Hars2 = 0610006H08Rik<br>
</i></span></div>
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style='text-align:left'><span style='font-size:200%;color:#E9EB5D'><i>is a
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style='text-align:left'><span style='font-size:200%;color:#E9EB5D'><i>statistic
(LRS) score</i></span><span style='font-size:267%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><i><br>
</i></span></span></layer></div>
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<td width="100%"></td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>When you do this you
will find that only the transcript 0610006H08Rik has a strong cis QTL. See
the slide above. The LRS peaks above 35<span style="mso-spacerun:
yes"> </span>(LOD of greater than 7.5). It turns out that this
transcript is really Hars2, also known as histydl tRNA synthase 2.</font><br>
</td>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0055.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0055.htm deleted file mode 100755 index 36b2d736..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0055.htm +++ /dev/null @@ -1,168 +0,0 @@ -<html>
<head>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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mapped</i></span></div>
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mso-text-raise:0%;mso-line-spacing:"100 50 0";mso-line-spacing:"100 50 0"'><span
style='font-size:117%;color:#FF0F0F'>C in B6, T in D2 </span><span
style='font-size:150%;color:black;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
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4'><i>no SNPs</i></span></div>
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<td width="100%"></td>
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<td align=left colspan=1><font face=Helvetica size=3>LetÕs look at Hars2 in
more detail by mapping all of the perfect match probes (16 of them) that
target this transcript.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Go back to the Trait
Data and Editing window and select Chr 2 (rather than ALL as shown above)
and also select PM Probes. Then click on Interval Mapping button.</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=Helvetica size=3>You will get the
illustration above, but without the sequence data that we have added.<span
style="mso-spacerun: yes"> </span>The 16 perfect match probes are
arranged in sequence (red is 5 prime, blue is the 3 prime end). For example,
the 5 prime-most primer 307387 has the sequence CACTG..... It also has a
polymorphism at the 17 nucleotide of this 25 nt probe sequence.</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=Helvetica size=3>How do we know that the
5 prime probe is polymorphic? By looking up the sequence in the Celera
Genomics databases which often contqains sequence data for C57BL/6J (B6
above) and for DBA/2J.<span style="mso-spacerun: yes"> </span>But two
blue probes (14 and 15) do NOT contain SNPs but still have very large LRS
scores. The other probes do not perform so wel. Highly variable probe
performance is probably a result of the very different stacking energies of
DNA-RNA duplexes.</font><br>
</td>
</tr>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0056.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0056.htm deleted file mode 100755 index 43ebf6d5..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0056.htm +++ /dev/null @@ -1,129 +0,0 @@ -<html>
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<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The vertical text says it
all: Even when using identical probes, mapping performance (and signal)
depends on tissue type and mRNA complexity. This is another gene in the
Hars2 interval. Forebrain and tem cell mRNAs were run on the same U74Av2
array, whereas the cerebellum mRNA was run on the 430A and 430B array set.</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 diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0057.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0057.htm deleted file mode 100755 index 9a7adf61..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0057.htm +++ /dev/null @@ -1,122 +0,0 @@ -<html>
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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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mso-text-indent-alt:0'><span style='font-size:68%'><i>Is there known biology to
link Hars2 with App? </i></span></div>
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<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%;
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<div><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>69 SNPs, 1
cSNP: <br>
</b></span></div>
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<div><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>6 exons in
NCBI, <br>
</b></span></div>
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<div><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'><b>2 exons in
Celera</b></span></div>
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<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%'><span style='font-family:"Gill Sans";font-size:250%;
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<td width="100%"></td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Hars2 is not a well
characterized gene and their is no biology yet to support the hypothesis
that Hars2 modulates gene expression, let alone App expression in specific.
There are also serious database/assembly discrepancies between Celera and
MGSCv3 regarding the genomic organization of this gene. But there appear to
be approximately 69 SNPs in Hars2, one of which results in a substitution.</font><br>
</td>
</tr>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm deleted file mode 100755 index 9feed242..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm +++ /dev/null @@ -1,135 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description
content="Jun-19-03: WebQTL link to www.webqtl.org/search.html">
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<body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};'
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<script> - -g_origHeight = 566; -g_origWidth = 755; -g_width = window.innerWidth - 10; -g_height = window.innerHeight - 10; - -g_top = 0; -g_left = 0; - -if ( g_width < ( g_origWidth * g_height /g_origHeight ) ) - g_height = g_width * g_origHeight / g_origWidth; -else - g_width = g_origWidth * g_height / g_origHeight; - -g_top = (window.innerHeight - g_height) / 2; -g_left = (window.innerWidth - g_width) / 2; - -document.write( '<layer id=SlideLayer BGCOLOR=#484848 background="" top=' + g_top + ' left=' + g_left + ' height=' + g_height + ' width=' + g_width + ' >' ); -document.SlideLayer.clip.top = 0; -document.SlideLayer.clip.left = 0; -document.SlideLayer.clip.height = g_height; -document.SlideLayer.clip.width = g_width; -function new_font_size() { - var size = 11 * g_width / g_origWidth; - if ( size < 1 ) size = 1; - return size+"pt"; -} -</script>
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<div><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.19 * g_height; mywidth = 0.93 * g_width; - 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 ";mso-margin-left-alt:232;
mso-text-indent-alt:0;mso-line-spacing:" 0 ";mso-margin-left-alt:232;
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style='text-align:left'><span style='font-size:68%'><i>WebQTL<span
style="mso-spacerun: yes"> </span><br>
</i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 0.89 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:68%'><i>link to <br>
</i></span></span></layer><script> - mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.08 * g_height; mywidth = 0.89 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:86%'><i>www.webqtl.org/search.html</i></span><span
style='font-size:68%;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></layer></div>
</layer></div>
</layer><script> - mytop = 0.36 * g_height; myleft = 0.02 * g_width; myheight = 0.45 * g_height; mywidth = 0.73 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.36 * g_height; mywidth = 0.71 * g_width; - 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:#FBFDB8;font-size:213%;
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style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute;
left:-8.06%;font-family:Times;font-size:99%'>1.</span></span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Discovering shared
expression </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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3'>patterns<br>
</span></span></layer></div>
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<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56'><script> - mytop = 0 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.55 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute;
left:-9.09%;font-family:Times;font-size:99%'>2.</span></span><span
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style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'>modulators (QTLs)<br>
</span></span></layer></div>
</layer><script> - mytop = 0.3 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.71 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:" 0 ";mso-margin-left-alt:348;mso-text-indent-alt:
56'><script> - mytop = 0 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.66 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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3'><span style='mso-special-format:numbullet;color:#FBFDB8;position:absolute;
left:-7.61%;font-family:Times;font-size:99%'>3.</span></span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Discovering downstream
targets</span></span></layer></div>
</layer></div>
</layer></div>
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<div></div>
</layer><script> - mytop = 0.65 * g_height; myleft = 0.65 * g_width; myheight = 0.1 * g_height; mywidth = 0.26 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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<layer>
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<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=Helvetica size=3>Part 3.<span
style="mso-spacerun: yes"> </span>Many investigators would like to
discover the set of downstream targets of a gene of interest.</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=Helvetica size=3>In a genetic and
functional sense, that question can only be addressed effectively if there
is genetic variation in the particular gene.<span style="mso-spacerun:
yes"> </span>We know that Fos is an important transcription factor,
but unless it is polymorphic between C57BL/6J and DBA/2J, then it cannot
generate a genetic variance signal with which we can work. We can still
study covariance of Fos and hundreds of other transcripts (an interesting
exercise), but there are no genetic causes-and-effects.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
-</script><script language=JavaScript><!--
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</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0059.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0059.htm deleted file mode 100755 index a479ea68..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0059.htm +++ /dev/null @@ -1,128 +0,0 @@ -<html>
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<meta name=ProgId content=PowerPoint.Slide>
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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<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 ";mso-line-spacing:" 0 "'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 1.07 * g_width; - 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> - mytop = 0.08 * g_height; myleft = 0.03 * g_width; myheight = 0.07 * g_height; mywidth = 0.85 * g_width; - 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> - mytop = 0.21 * g_height; myleft = 0.02 * g_width; myheight = 0.15 * g_height; mywidth = 0.84 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script> - mytop = 0.04 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span
style='font-size:64%'><i>What are targets of the Hars2 polymorphisms?</i></span><span
style='font-size:82%;mso-special-format:lastCR;display:none'><br>
</span></div>
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<div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>App
and many other<br>
</i></span></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.51 * g_width; - 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> - mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.43 * g_width; - 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"> </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() { - -} -//-->
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm deleted file mode 100755 index aa804b9a..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm +++ /dev/null @@ -1,134 +0,0 @@ -<html>
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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span
style='font-size:82%'><i>Direct correlations between genotypes and traits</i></span><span
style='font-size:82%;mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.22 * g_height; myleft = 0.03 * g_width; myheight = 0.42 * g_height; mywidth = 0.34 * g_width; - 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; - 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<br>
</i></span></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; - 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 traits </i></span></span></layer><script> - mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; - 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>would be obvious </i></span></span></layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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color:#E9EB5D'><i>candidates to </i></span></span></layer><script> - mytop = 0.28 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%;
color:#E9EB5D'><i>D2Mit423</i></span></span></layer></div>
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-1<br>
</i></span></div>
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1</i></span></div>
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<td align=left colspan=1><font face=Verdana size=3>We can review the set of
correlations between the marker D2Mit423 and all transcripts in
forebrain.<span style="mso-spacerun: yes"> </span>This is in essence a
backwards way of mapping QTLs. We are considering one marker and asking what
traits correlate to the marker and how well.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm deleted file mode 100755 index cce3b81c..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm +++ /dev/null @@ -1,124 +0,0 @@ -<html>
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<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 10">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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style='font-size:82%'><i>WhatÕs downstream of Chr 2 near Hars2?</i></span><span
style='font-size:82%;mso-special-format:lastCR;display:none'><br>
</span></div>
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mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span
style='font-size:64%'><i>Notice many Chr 2 hits: Linkage disequilibrium limits
specificity</i></span><span style='font-size:64%;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.27 * g_height; myleft = 0.07 * g_width; myheight = 0.17 * g_height; mywidth = 0.22 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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<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%'><span style='font-size:150%;color:#FF0F0F'><b>Click here</b></span></div>
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<td width="100%"></td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The marker D2Mit423
correlates moderately well with a number of Chr 2 transcripts. This is due
to linkage disequilibrium. These correlations are not due to a molecular
interactions other than being close together on a chromosome.<span
style="mso-spacerun: yes"> </span>But we have circled one transcript,
actinin alpha 2, that has a moderately good correlation (0.59) with
D2Mit423. If we map this gene we expect to find a suggestive QTL that peaks
near D2Mit423</font><br>
</td>
</tr>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0062.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0062.htm deleted file mode 100755 index c8c24f70..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0062.htm +++ /dev/null @@ -1,96 +0,0 @@ -<html>
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<div><script> - mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.95 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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mso-text-raise:0%;mso-line-spacing:" 0 ";mso-line-spacing:" 0 "'><span
style='font-size:82%'><i>WhatÕs downstream of Chr 2 near Hars2?</i></span><span
style='font-size:82%;mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.12 * g_height; myleft = 0.07 * g_width; myheight = 0.75 * g_height; mywidth = 0.61 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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<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%'><span style='font-family:"Gill Sans";font-size:233%;
color:#E9EB5D'><i>modest support that Actn2 is modulated by the Hars2 region</i></span></div>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>There is some support for
the hypothesis that Actn2 is downstream of a polymorphism in the Hars2
region. But again, due to the 10 to 20 Mb precision of the mapping data,
this relation could be generated by a large number of other polymorphisms
close to Hars2. In the absence of a biological connection between Actn2 and
Hars2 we have a weak hypothesis. If there were a plausible functional
connection between the two genes, then this hypothesis could be quickly
upgraded.</font><br>
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\ No newline at end of file diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0063.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0063.htm deleted file mode 100755 index 53358da8..00000000 --- a/web/tutorial/ppt/WebQTLDemo_files/slide0063.htm +++ /dev/null @@ -1,139 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
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genomics</title>
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<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
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<div><script> - mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.92 * g_width; - 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 ";mso-line-spacing:" 0 "'><span
style='font-size:73%'><i>Does Hars2 correlate with Actn2 strongly?</i></span><span
style='font-size:82%;mso-special-format:lastCR;display:none'><br>
</span></div>
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</layer><script> - mytop = 0.07 * g_height; myleft = 0.02 * g_width; myheight = 0.28 * g_height; mywidth = 0.47 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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<div><script language=JavaScript><!--
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<div><script language=JavaScript><!--
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<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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.26 * g_width; - 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>Plenty of high </i></span></span></layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.25 * g_width; - 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>correlations, </i></span></span></layer><script> - mytop = 0.14 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.25 * g_width; - 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>including 2 </i></span></span></layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.28 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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<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%'><span style='font-family:"Gill Sans";font-size:267%;
color:#E9EB5D'><i>Sort by gene</i></span></div>
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<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>We can test the Hars2 to
Actn2 connection directly. This process weakens the putative association. We
are ready to move on and examine other candidates in the Hars2 region near
D2Mit423.<span style="mso-spacerun: yes"> </span>Or in your case,
please start from the beginning using other genes and transcripts and
tissues that interest you more than this App-Hsp84-Hars2 example.</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>This concludes the first
demonstation of how to use some of the WebQTL features. Please explore.
Please also send feedback for improvements or additions to
rwilliam@nb.utmem.edu</font><br>
</td>
</tr>
</table>
</div>
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<script language=JavaScript><!--
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</span></div>
</layer></div>
</layer><script> - mytop = 0.12 * g_height; myleft = 0.06 * g_width; myheight = 0.32 * g_height; mywidth = 0.9 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%;
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</span></span></layer><script> - mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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</span></span></layer><script> - mytop = 0.24 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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<tr>
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<td align=left colspan=1><font face=Verdana size=3>END</font><br>
</td>
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</table>
</div>
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-//-->
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