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<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 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 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 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 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 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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upstream modulatory loci</font></a></b></font></td>
</tr>
</table>
<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>WebQTL searches for upstream
controllers</a></b></font></td>
</tr>
</table>
<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>Genetic versus Physical maps
for App expression</a></b></font></td>
</tr>
</table>
<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>Physical map for distal
chromosome 7</a></b></font></td>
</tr>
</table>
<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>Evaluating candidate genes</a></b></font></td>
</tr>
</table>
<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>Physical maps are zoomable</a></b></font></td>
</tr>
</table>
<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>Evaluating Ctbp2 as a
candidate QTL for App</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>Evaluating Ctbp2 using
other resources</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>"Summary of Part 2"</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>Test Questions</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>Contact for comments and
improvements:</a></b></font></td>
</tr>
</table>
</body>
</html>
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href="webqtl_demo2.ppt.ppt">
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<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>The GeneNetwork and WebQTL :
PART 2<span style="mso-spacerun: yes"> </span><br>
link to www.genenetwork.org</a></b></font></td>
</tr>
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<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 study expression
variation and genetic correlation (slides 2–17)</font></td>
</tr>
<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators
(slides 18–29)</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>Slide 2</a></b></font></td>
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<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>Slide 3</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><font face=Verdana>Discovering
upstream modulatory loci</font></a></b></font></td>
</tr>
</table>
<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>WebQTL searches for upstream
controllers</a></b></font></td>
</tr>
</table>
<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>Genetic versus Physical maps
for App expression</a></b></font></td>
</tr>
</table>
<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>Physical map for distal
chromosome 7</a></b></font></td>
</tr>
</table>
<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>Evaluating candidate genes</a></b></font></td>
</tr>
</table>
<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>Physical maps are zoomable</a></b></font></td>
</tr>
</table>
<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>Evaluating Ctbp2 as a
candidate QTL for App</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>Evaluating Ctbp2 using
other resources</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>"Summary of Part 2"</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>Summary of Part 2</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>Test Questions</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>Contact for comments and
improvements:</a></b></font></td>
</tr>
</table>
</body>
</html>
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- else if( (event.which == 32) || (event.which == 13) || HitOK( event ) ) { - if( window.name == "PPTSld" ) - parent.PPTSld.DocumentOnClick(); - else - parent.M_GoNextSld(); - } - else if ( parent.IsFullScrMode() && ((event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12)) ) - parent.M_GoNextSld(); - else if ( parent.IsFullScrMode() && ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8)) ) - parent.M_GoPrevSld(); - - return; - } - - if( IsNts() ) return; - - if(parent.IsFullScrMode() && event.keyCode == 27 && !parent.HideMenu() ) - parent.base.CloseFullScreen(); - else if( (event.keyCode == 32) || (event.keyCode == 13) ) - { - if( window.name == "PPTSld" ) - parent.PPTSld.DocumentOnClick(); - else - parent.M_GoNextSld(); - } - else if ( parent.IsFullScrMode() && ((event.keyCode == 78) || (event.keyCode == 110)) ) - parent.M_GoNextSld(); - else if ( parent.IsFullScrMode() && ((event.keyCode == 80) || (event.keyCode == 112)) ) - parent.M_GoPrevSld(); -} - -function DocumentOnClick(event) -{ - if ( g_doAdvOnClick && !parent.IsFullScrMode() ) { - parent.base.TP_GoToNextSld(); - return; - } - - if ( parent.base.msie < 0 ) - { - if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || - (event && ( (event.which == 32) || (event.which == 13) ) ) ) - parent.M_GoNextSld(); - return; - } - if( IsNts() || (parent.IsFullScrMode() && parent.HideMenu() ) ) return; - if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || - (event && ( (event.keyCode==32) || (event.keyCode == 13) ) ) ) - parent.M_GoNextSld(); -} -
- -var g_supportsPPTHTML = SupportsPPTHTML(), g_scaleInFrame = true, gId="", g_bgSound="", - g_scaleHyperlinks = false, g_allowAdvOnClick = true, g_showInBrowser = false, g_doAdvOnClick = false; - - var g_showAnimation = 0; -var g_hasTrans = false, g_autoTrans = false, g_transSecs = 0; -var g_animManager = null; - -var ENDSHOW_MESG="End of slide show, click to exit.", SCREEN_MODE="Frames", gIsEndShow=0, NUM_VIS_SLDS=14, SCRIPT_HREF="script.js", FULLSCR_HREF="fullscreen.htm"; -var gCurSld = gPrevSld = 1, g_offset = 0, gNtsOpen = gHasNts = gOtlTxtExp = gNarrationPaused = false, gOtlOpen = true -window.gPPTHTML=SupportsPPTHTML() -var g_hideNav = 0; -function UpdNtsPane(){ PPTNts.location.replace( MHTMLPrefix+GetHrefObj( gCurSld ).mNtsHref ) } -function UpdNavPane( sldIndex ){ if(gNavLoaded) PPTNav.UpdNav() } -function UpdOtNavPane(){ if(gOtlNavLoaded) PPTOtlNav.UpdOtlNav() } -function UpdOtlPane(){ if(gOtlLoaded) PPTOtl.UpdOtl() } -function SetHasNts( fVal ) -{ - if( gHasNts != fVal ) { - gHasNts=fVal - UpdNavPane() - } -} - -function ToggleVNarration() -{ - if ( base.msie < 0 ) { - PPTSld.ToggleSound( false, PPTSld.document.NSPlay ); - return; - } - - rObj=PPTSld.document.all("NSPlay") - if( rObj ) { - if( gNarrationPaused ) - rObj.Play() - else - rObj.Pause() - - gNarrationPaused=!gNarrationPaused - } -} - -function PrevSldViewed(){ GoToSld( GetHrefObj(gPrevSld).mSldHref ) } -function HasPrevSld() { return ( gIsEndShow || ( g_currentSlide != 1 && GetHrefObj( g_currentSlide-1 ).mVis == 1 )||( GetCurrentSlideNum() > 1 ) ) } -function HasNextSld() { return (GetCurrentSlideNum() != GetNumSlides()) } -function StartEndShow() -{ -// g_hideNav = 1; -// PPTNav.location.reload(); - if( PPTSld.event ) PPTSld.event.cancelBubble=true - - doc=PPTSld.document - doc.open() - doc.writeln('<html><head><script > /*defer>*/ g_ctxmenu = 0; ' + - 'if( parent.base.msie < 0 ) { document.captureEvents(Event.KEYPRESS); document.captureEvents(Event.MOUSEDOWN); document.onkeypress = _KPH; document.onmousedown = _KPH; } ' + - 'function DocumentOnClick(event) { return _KPH(event); } function IsContextMenu() { return (g_ctxmenu ==1); } ' + - 'function _KPH(event)' + - '{ ' + - 'if ( parent.base.msie < 0 && (parent.IsFullScrMode() ) && event ) { if ( (!parent.IsMac() && event.which == 3) || ( parent.IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { return parent.KPH(event); } ' + - ' else if (event.which == 27 || event.which == 32 || event.which == 13 || parent.HitOK( event ) || (event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12) ) { if ( IsContextMenu() ) { return parent.KPH(event); } parent.base.CloseFullScreen(); return; } ' + - ' else if ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8) ) { parent.M_GoPrevSld(); } } ' + - 'if( parent.HideMenu() ) return; if( (parent.IsFullScrMode() ) && event) { if ( (event.keyCode==27 || event.keyCode == 13 || event.keyCode==32 || event.type=="click" ) || (event.keyCode == 78) || (event.keyCode == 110) ) { parent.base.CloseFullScreen(); }' + - ' else if ( (event.keyCode == 80) || (event.keyCode == 112) ) { parent.M_GoPrevSld(); } } } function Unload() { parent.gIsEndShow=0; } function SetupEndShow() { if ( !parent.IsFullScrMode() ) { return; } else { parent.PPTNav.location.reload(); } parent.gIsEndShow=1; if ( parent.g_docTable[0].type != "jpeg" ) { if ( parent.base.msie < 0 ) {parent.createCM(); } document.oncontextmenu=parent._CM; } }</script></head><body scroll=\"no\" onclick=\"DocumentOnClick(event)\" onkeypress=\"_KPH(event)\" bgcolor=\"black\" onload=\"SetupEndShow()\" onunload=\"Unload()\"><center><p><font face=Tahoma color=white size=2><br><b>' + ENDSHOW_MESG + '</b></font></p></center></body></html>') - doc.close() -} -function SetSldVisited(){ gDocTable[gCurSld-1].mVisited=true } -function IsSldVisited(){ return gDocTable[gCurSld-1].mVisited } -function hrefList( sldHref, visible, sldIdx ) -{ - this.mSldHref= this.mNtsHref = sldHref - this.mSldIdx = sldIdx - this.mOrigVis= this.mVis = visible - this.mVisited= false -} -var gDocTable = new Array(
- new hrefList("slide0001.htm", 1, 1),
- new hrefList("slide0002.htm", 1, 2),
- new hrefList("slide0003.htm", 1, 3),
- new hrefList("slide0004.htm", 1, 4),
- new hrefList("slide0005.htm", 1, 5),
- new hrefList("slide0006.htm", 1, 6),
- new hrefList("slide0007.htm", 1, 7),
- new hrefList("slide0008.htm", 1, 8),
- new hrefList("slide0009.htm", 1, 9),
- new hrefList("slide0010.htm", 1, 10),
- new hrefList("slide0011.htm", 1, 11),
- new hrefList("slide0012.htm", 1, 12),
- new hrefList("slide0013.htm", 1, 13),
- new hrefList("slide0014.htm", 1, 14)
-);
- -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( 11,0,1);
-makeSlide( 12,0,1);
-makeSlide( 13,1,1);
- -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 = 14, - 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("/") ) + "/" + "webqtl_demo2.ppt_files"; -var g_showoutline = 1; -var g_shownotes = includeNotes; -var g_currentSlide = INITSLIDENUM, g_prevSlide = INITSLIDENUM; 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<head>
<meta http-equiv=Content-Type content="text/html; charset=macintosh">
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<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2.ppt.ppt">
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<meta name=Description
content="Aug-15-05: The GeneNetwork and WebQTL : PART 2 link to www.genenetwork.org">
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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.png" 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:96.15%;height:18.19%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232;
mso-text-indent-alt:0;position:absolute;top:11.65%;left:.96%;width:98.2%;
height:73.78%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-size:73%'>The GeneNetwork and WebQTL : PART 2<span
style="mso-spacerun: yes"> </span><br>
</span></span><span
style='position:absolute;top:48.68%;left:4.34%;width:95.23%'><span
style='font-size:73%'>link to www.genenetwork.org</span><span style='font-size:
73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
</div>
<div style='position:absolute;top:24.02%;left:5.82%;width:54.03%;height:68.55%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='position:absolute;top:0%;left:3.67%;width:96.32%;
height:61.34%'>
<div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:0%;width:100.0%;height:51.68%'><span
style='position:absolute;top:0%;left:0%;width:89.05%'><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 study </span></span><span style='position:absolute;top:23.57%;
left:9.66%;width:79.13%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'>expression variation </span></span><span style='position:absolute;
top:47.15%;left:9.66%;width:90.33%'><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3'>and genetic correlation </span></span><span
style='position:absolute;top:70.73%;left:9.66%;width:79.13%'><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'>(slides 2–17)<br>
</span></span></div>
<div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:60.5%;left:0%;width:93.63%;height:39.91%'><span
style='position:absolute;top:0%;left:0%;width:95.1%'><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 </span></span><span style='position:absolute;top:30.52%;
left:10.32%;width:89.67%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'>upstream modulators </span></span><span style='position:absolute;top:61.05%;
left:10.32%;width:84.51%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'>(slides 18–29)</span></span></div>
</div>
</div>
<img border=0 src="slide0001_image001.png" 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:"-346 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:"-346 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:96.15%;height:18.19%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div>
<img border=0 src="slide0001_image002.png" style='position:absolute;top:50.53%;
left:48.74%;width:25.56%;height:13.07%'></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: Discovering
upstream modulators and quantitative trait loci (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>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Part 2: Discovering
upstream modulators and quantitative trait loci (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>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
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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.png" 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:"-134 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:"-134 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:29.4%;
height:5.83%'>
<div style='text-align:center;mso-line-spacing:"-134 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:"-134 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:-5.43%;width:105.96%;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:92.06%'>
<div style='text-align:center;mso-line-spacing:"-240 0 0";mso-margin-left-alt:
16;mso-text-indent-alt:16;position:absolute;top:0%;left:0%;width:100.0%;
height:65.51%'><span style='font-family:Arial;font-size:267%;color:#E9EB5D'>How
to make recombinant inbred strains (RI)</span><span style='font-family:Arial;
font-size:150%;color:aqua;display:none'><br>
</span></div>
<div style='text-align:center;mso-line-spacing:"-160 0 0";mso-margin-left-alt:
16;mso-text-indent-alt:16;position:absolute;top:62.06%;left:6.37%;width:87.37%;
height:37.93%'><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="slide0002_image003.png" style='position:absolute;top:28.79%;
left:45.43%;width:18.14%;height:1.06%'><img border=0
src="slide0002_image004.png" 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:9.71%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:9.09%;left:6.8%;width:93.19%;
height:81.81%'>
<div style='mso-line-spacing:"-173 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:"-173 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="slide0002_image005.png" 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:9.71%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:9.09%;left:8.0%;width:92.8%;
height:81.81%'>
<div style='mso-line-spacing:"-173 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:"-173 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="slide0002_image006.png" style='position:absolute;top:20.31%;
left:66.62%;width:4.23%;height:11.83%'><img border=0
src="slide0002_image007.png" style='position:absolute;top:35.51%;left:23.97%;
width:50.86%;height:1.23%'><img border=0 src="slide0002_image008.png"
style='position:absolute;top:35.68%;left:24.1%;width:.66%;height:4.06%'><img
border=0 src="slide0002_image009.png" style='position:absolute;top:35.68%;
left:40.92%;width:.52%;height:4.06%'><img border=0 src="slide0002_image010.png"
style='position:absolute;top:35.68%;left:57.61%;width:.52%;height:4.06%'><img
border=0 src="slide0002_image011.png" 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:6.49%;height:12.36%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:8.57%;left:20.4%;width:73.46%;
height:84.28%'>
<div style='mso-line-spacing:"-230 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:"-230 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="slide0002_image012.png" style='position:absolute;top:39.92%;
left:22.25%;width:4.23%;height:11.83%'><img border=0
src="slide0002_image013.png" style='position:absolute;top:39.92%;left:38.94%;
width:4.23%;height:11.83%'><img border=0 src="slide0002_image014.png"
style='position:absolute;top:39.92%;left:55.62%;width:4.23%;height:11.83%'><img
border=0 src="slide0002_image015.png" style='position:absolute;top:39.39%;
left:72.84%;width:4.23%;height:11.83%'><img border=0
src="slide0002_image016.png" style='position:absolute;top:43.46%;left:43.97%;
width:11.12%;height:3.53%'><img border=0 src="slide0002_image017.png"
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:20.26%;height:26.67%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:12.58%;left:6.53%;width:88.23%;
height:83.44%'>
<div style='text-align:center;mso-line-spacing:"-269 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:99.25%'><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:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:73.8%;left:0%;width:99.25%;
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="slide0002_image018.png" style='position:absolute;top:60.95%;
left:50.72%;width:9.93%;height:3.53%'><img border=0 src="slide0002_image019.png"
style='position:absolute;top:62.72%;left:54.03%;width:4.37%;height:28.97%'><img
border=0 src="slide0002_image020.png" style='position:absolute;top:61.13%;
left:79.86%;width:10.86%;height:3.53%'><img border=0
src="slide0002_image021.png" 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:9.27%;height:9.71%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:9.09%;left:12.85%;width:85.71%;
height:81.81%'>
<div style='mso-line-spacing:"-173 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:"-173 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:9.27%;height:9.71%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:9.09%;left:12.85%;width:85.71%;
height:81.81%'>
<div style='mso-line-spacing:"-173 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:"-173 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:5.65%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:15.62%;left:12.04%;width:87.95%;
height:68.75%'><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:17.49%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:6.06%;left:7.46%;width:92.53%;
height:88.88%'>
<div style='mso-line-spacing:"-341 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:"-341 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:6.49%;height:12.36%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:7.14%;left:20.4%;width:73.46%;
height:84.28%'>
<div style='mso-line-spacing:"-230 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:"-230 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="slide0002_image022.png" style='position:absolute;top:54.24%;
left:18.01%;width:75.62%;height:1.06%'><img border=0
src="slide0002_image023.png" style='position:absolute;top:54.06%;left:17.88%;
width:.66%;height:3.88%'><img border=0 src="slide0002_image024.png"
style='position:absolute;top:54.24%;left:32.45%;width:.52%;height:3.88%'><img
border=0 src="slide0002_image025.png" style='position:absolute;top:54.24%;
left:48.07%;width:.52%;height:4.06%'><img border=0 src="slide0002_image026.png"
style='position:absolute;top:54.24%;left:62.78%;width:.52%;height:4.06%'><img
border=0 src="slide0002_image027.png" style='position:absolute;top:54.24%;
left:77.74%;width:.52%;height:4.06%'><img border=0 src="slide0002_image028.png"
style='position:absolute;top:54.59%;left:92.71%;width:.52%;height:3.71%'><img
border=0 src="slide0002_image029.png" style='position:absolute;top:44.87%;
left:49.13%;width:.79%;height:10.07%'><img border=0 src="slide0002_image030.png"
style='position:absolute;top:57.59%;left:15.89%;width:4.23%;height:11.83%'><img
border=0 src="slide0002_image031.png" style='position:absolute;top:57.59%;
left:30.86%;width:4.37%;height:11.83%'><img border=0
src="slide0002_image032.png" style='position:absolute;top:57.59%;left:46.35%;
width:4.23%;height:11.83%'><img border=0 src="slide0002_image033.png"
style='position:absolute;top:57.59%;left:60.92%;width:4.23%;height:11.83%'><img
border=0 src="slide0002_image034.png" style='position:absolute;top:57.59%;
left:75.62%;width:4.23%;height:11.83%'><img border=0
src="slide0002_image035.png" style='position:absolute;top:57.59%;left:90.86%;
width:4.23%;height:11.83%'><img border=0 src="slide0002_image036.png"
style='position:absolute;top:84.09%;left:56.42%;width:1.98%;height:1.41%'><img
border=0 src="slide0002_image037.png" style='position:absolute;top:80.21%;
left:25.96%;width:1.98%;height:11.83%'><img border=0
src="slide0002_image038.png" 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:13.9%;height:13.78%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:7.69%;left:.95%;width:99.04%;
height:85.89%'>
<div style='text-align:center;mso-line-spacing:"-173 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:"-173 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:"-173 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="slide0002_image039.png" style='position:absolute;top:12.36%;
left:14.17%;width:10.59%;height:6.36%'><img border=0
src="slide0002_image040.png" 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:9.53%;height:13.78%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:7.69%;left:6.94%;width:88.88%;
height:85.89%'>
<div style='text-align:center;mso-line-spacing:"-173 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:"-173 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:"-173 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:11.78%;height:9.71%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:9.09%;left:3.37%;width:94.38%;
height:81.81%'>
<div style='text-align:center;mso-line-spacing:"-173 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:"-173 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:12.18%;height:13.78%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:7.69%;left:2.17%;width:95.65%;
height:85.89%'>
<div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.95%;width:84.09%;
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:"-173 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:"-173 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.95%;width:84.09%;
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:21.98%;height:21.73%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:4.06%;left:5.42%;width:89.15%;
height:91.86%'>
<div style='text-align:center;mso-line-spacing:"-173 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:"-173 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:9.71%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:9.09%;left:12.65%;width:87.34%;
height:81.81%'>
<div style='mso-line-spacing:"-173 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:"-173 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:7.94%;height:9.71%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:9.09%;left:15.0%;width:83.33%;
height:81.81%'>
<div style='mso-line-spacing:"-173 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:"-173 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:9.71%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:16.36%;left:6.12%;width:93.19%;
height:74.54%'>
<div style='mso-line-spacing:"-173 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:"-173 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="slide0002_image041.png" 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:9.8%;height:14.13%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:5.0%;left:5.4%;width:90.54%;
height:87.5%'>
<div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:8.95%;width:82.08%;
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:"-134 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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:50.0%;left:4.47%;width:89.55%;
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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:75.71%;left:8.95%;width:82.08%;
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="slide0002_image042.png" style='position:absolute;top:79.32%;
left:83.84%;width:1.98%;height:11.83%'><img border=0
src="slide0002_image043.png" style='position:absolute;top:84.8%;left:83.7%;
width:1.85%;height:2.12%'><img border=0 src="slide0002_image044.png"
style='position:absolute;top:79.85%;left:53.5%;width:1.98%;height:11.83%'><img
border=0 src="slide0002_image045.png" style='position:absolute;top:83.92%;
left:53.5%;width:1.98%;height:1.41%'><img border=0 src="slide0002_image046.png"
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:9.54%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:11.11%;left:9.61%;width:90.38%;
height:79.62%'><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="slide0002_image047.png" style='position:absolute;top:27.2%;
left:32.98%;width:31.39%;height:4.06%'><img border=0
src="slide0002_image048.png" style='position:absolute;top:66.25%;left:60.92%;
width:1.98%;height:3.18%'><img border=0 src="slide0002_image049.png"
style='position:absolute;top:64.31%;left:15.89%;width:1.98%;height:5.3%'><img
border=0 src="slide0002_image050.png" style='position:absolute;top:57.59%;
left:75.62%;width:1.98%;height:5.65%'><img border=0 src="slide0002_image051.png"
style='position:absolute;top:28.44%;left:48.87%;width:.92%;height:8.12%'><img
border=0 src="slide0002_image052.png" style='position:absolute;top:62.19%;
left:23.84%;width:3.57%;height:16.96%'><img border=0
src="slide0002_image053.png" 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 few slides
provide a short introduction to mapping the loci that are responsible for
variation in a trait such as App expression level. These modulatory regions
of the genome are sometimes called quantitative trait loci or QTLs. You may
want to do some independent reading on this topic if this is your first
exposure to QTL analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The genetic reference
population (GRP) of BXD recombinant inbred strains were originally generated
about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed
female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny.
At the bottom of this slide we have schematized one chromosome pair from
three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The
dashed vertical lines that lead to the final BXD RI lines involve 21 full sib
matings (about 7 years of breeding). Some lines die out during inbreeding.
For example, there is no longer any BXD3 strain.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>1. Over the last decade,
our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at
Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD
strains. They have all been genotyped using about 13,700 markers (SNPs and
microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ
regions of the chromosomes as shown in the figure above.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. Chromosomes of RI GRPs
usually have about 4 times as many recombinations as those of F2 animals.
However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50
RI strains contain as many recombinations as 100 F2 animals.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. BXD43 through BXD100
were generated using a special method that resulted in a further doubling of
the average recombination density per chromosome. The entire set of 80 BXDs
therefore contains as many recombinations as about 260 F2 animals.</font><br>
</td>
</tr>
</table>
</div>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
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<td width="100%"></td>
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<td align=left colspan=1><font face=Verdana size=2>The next few slides
provide a short introduction to mapping the loci that are responsible for
variation in a trait such as App expression level. These modulatory regions
of the genome are sometimes called quantitative trait loci or QTLs. You may
want to do some independent reading on this topic if this is your first
exposure to QTL analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>The genetic reference
population (GRP) of BXD recombinant inbred strains were originally generated
about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed
female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny.
At the bottom of this slide we have schematized one chromosome pair from
three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The
dashed vertical lines that lead to the final BXD RI lines involve 21 full sib
matings (about 7 years of breeding). Some lines die out during inbreeding.
For example, there is no longer any BXD3 strain.</font><br>
</td>
</tr>
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<td align=left colspan=1><font face=Verdana size=2>Notes:</font><br>
</td>
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<td align=left colspan=1><font face=Verdana size=2>1. Over the last decade,
our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at
Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD
strains. They have all been genotyped using about 13,700 markers (SNPs and
microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ
regions of the chromosomes as shown in the figure above.</font><br>
</td>
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<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2. Chromosomes of RI GRPs
usually have about 4 times as many recombinations as those of F2 animals.
However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50
RI strains contain as many recombinations as 100 F2 animals.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>3. BXD43 through BXD100
were generated using a special method that resulted in a further doubling of
the average recombination density per chromosome. The entire set of 80 BXDs
therefore contains as many recombinations as about 260 F2 animals.</font><br>
</td>
</tr>
</table>
</body>
</html>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
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<body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)"
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img
border=0 src="slide0003_image054.png" 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:"-126 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:"-126 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="slide0003_image055.png" 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:"-126 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:"-126 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:19.43%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:10.0%;left:5.1%;width:95.4%;
height:84.54%'>
<div style='mso-line-spacing:"-384 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:"-384 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:19.43%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:10.9%;left:5.18%;width:94.81%;
height:84.54%'>
<div style='mso-line-spacing:"-384 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:"-384 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="slide0003_image056.png" style='position:absolute;top:17.31%;
left:31.25%;width:1.32%;height:42.22%'><img border=0
src="slide0003_image057.png" style='position:absolute;top:40.63%;left:31.39%;
width:39.86%;height:3.53%'>
<div style='position:absolute;top:20.67%;left:38.27%;width:30.19%;height:26.32%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:6.04%;left:4.38%;width:92.1%;
height:89.93%'>
<div style='mso-line-spacing:"-320 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:0%;left:0%;width:100.0%;height:58.2%'><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:53.84%;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:"-422 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16;position:absolute;top:61.19%;left:0%;width:100.0%;height:38.8%'><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:21.05%;height:19.43%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:10.0%;left:6.28%;width:88.67%;
height:84.54%'>
<div style='mso-line-spacing:"-384 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:"-384 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:21.05%;height:19.43%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:10.9%;left:6.28%;width:88.67%;
height:84.54%'>
<div style='mso-line-spacing:"-384 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:"-384 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="slide0003_image058.png" 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:"-350 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:"-350 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:"-350 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:"-350 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:79.5%;left:5.43%;width:104.1%;height:13.6%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='mso-line-spacing:"-256 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:3.89%;left:1.27%;width:98.72%;
height:93.5%'><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:34.72%;left:0%;width:99.74%'><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'>.</span></span></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:"-233 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:"-233 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:"-233 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:16.95%;height:17.84%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:3.96%;left:7.03%;width:85.15%;
height:92.07%'>
<div style='mso-line-spacing:"-350 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:"-350 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:6.35%;height:17.84%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:3.96%;left:20.83%;width:75.0%;
height:92.07%'>
<div style='mso-line-spacing:"-350 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:"-350 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:5.96%;height:17.84%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:3.96%;left:20.0%;width:71.11%;
height:92.07%'>
<div style='mso-line-spacing:"-350 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:"-350 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:12.54%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:5.63%;left:7.43%;width:91.73%;
height:87.32%'>
<div style='mso-line-spacing:"-233 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:"-233 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="slide0003_image059.png" 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:"-272 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:"-272 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:113.37%;height:6.36%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='mso-line-spacing:"-200 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;position:absolute;top:11.11%;left:1.16%;width:98.83%;
height:75.0%'><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="slide0003_image060.png" style='position:absolute;top:37.98%;
left:8.6%;width:13.77%;height:20.67%'>
<div class=O style='position:absolute;top:40.28%;left:10.99%;width:1.72%;
height:11.48%'>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
font-size:233%;color:white'><b></b></span><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:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:50.76%;left:7.69%;width:84.61%;
height:50.76%'><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:40.63%;left:18.41%;width:1.72%;
height:11.48%'>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
font-size:233%;color:white'><b></b></span><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:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:49.23%;left:7.69%;width:84.61%;
height:50.76%'><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="slide0003_image061.png" style='position:absolute;top:33.74%;
left:8.6%;width:13.77%;height:20.67%'>
<div class=O style='position:absolute;top:36.39%;left:18.41%;width:1.72%;
height:11.48%'>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
font-size:233%;color:white'><b></b></span><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:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:49.23%;left:7.69%;width:84.61%;
height:50.76%'><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:36.04%;left:10.99%;width:1.72%;
height:11.48%'>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%;
height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
font-size:233%;color:white'><b></b></span><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:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17;position:absolute;top:49.23%;left:7.69%;width:84.61%;
height:50.76%'><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:"-269 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:"-269 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="slide0003_image062.png" 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:20.92%;height:12.54%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:5.63%;left:6.32%;width:94.3%;
height:87.32%'>
<div style='mso-line-spacing:"-233 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:"-233 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 major types of QTLs that modulate variability in
transcript-relative steady state 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 binding of a
transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms
in enhancers or may be in 3Õ UTR binding sites that affect message stability.</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 fairly 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 overlapping
arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in
which an upstream polymorphism influences a downstream difference in mRNA
abundance can be 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>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
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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=Helvetica size=2>This slide is
illustrates two major types of QTLs that modulate variability in
transcript-relative steady state 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 binding of a
transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms
in enhancers or may be in 3Õ UTR binding sites that affect message stability.</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 fairly 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 overlapping
arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in
which an upstream polymorphism influences a downstream difference in mRNA
abundance can be 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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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href="webqtl_demo2.ppt.ppt">
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<meta name=Description content="Aug-15-05: Discovering upstream modulatory loci">
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img
border=0 src="slide0004_image063.png" style='position:absolute;top:38.86%;
left:5.03%;width:84.9%;height:45.75%'>
<div style='position:absolute;top:5.47%;left:2.51%;width:93.64%;height:8.65%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:20.4%;
left:1.41%;width:97.31%;height:75.51%'><span style='font-family:Verdana;
font-size:64%'>Discovering upstream modulatory loci</span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
</div>
<img border=0 src="slide0004_image064.png" style='position:absolute;top:20.31%;
left:18.01%;width:19.2%;height:25.97%'><img border=0
src="slide0004_image065.png" style='position:absolute;top:32.5%;left:78.01%;
width:19.2%;height:25.97%'></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>Please bring the Trait
Data and Analysis window to the front and look for the Interval Mapping
button. 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 Mapping Scale is
set to GENETIC</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Options: Permutation test
YES<span style="mso-spacerun: yes"> </span>(2000 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 (2000 is the default number)</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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2.ppt.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>Please bring the Trait
Data and Analysis window to the front and look for the Interval Mapping
button. 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 Mapping Scale is
set to GENETIC</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Options: Permutation test
YES<span style="mso-spacerun: yes"> </span>(2000 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 (2000 is the default number)</font><br>
</td>
</tr>
</table>
</body>
</html>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href="webqtl_demo2.ppt.ppt">
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<meta name=Description
content="Aug-15-05: WebQTL searches for upstream controllers">
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-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; -//-->
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:-.53%;left:1.72%;width:101.19%;height:8.65%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:98.95%;
height:75.51%'><span style='font-family:Verdana;font-size:64%'><i>WebQTL
searches for upstream controllers</i></span><span style='font-family:Verdana;
font-size:73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</div>
<div style='position:absolute;top:71.02%;left:34.96%;width:45.96%;height:19.78%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:3.57%;left:2.3%;width:97.69%;
height:91.96%'><span style='position:absolute;top:0%;left:0%;width:98.82%'><span
style='font-size:167%;color:#E9EB5D'><i>App maps on Chr 16 (blue </i></span></span><span
style='position:absolute;top:25.24%;left:0%;width:100.0%'><span
style='font-size:167%;color:#E9EB5D'><i>arrow points to the orange </i></span></span><span
style='position:absolute;top:49.51%;left:0%;width:86.72%'><span
style='font-size:167%;color:#E9EB5D'><i>triangle) but the best </i></span></span><span
style='position:absolute;top:74.75%;left:0%;width:86.72%'><span
style='font-size:167%;color:#E9EB5D'><i>locus is on Chr 7.</i></span><span
style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
</div>
<img border=0 src="slide0005_image066.png" style='position:absolute;top:8.83%;
left:1.19%;width:98.27%;height:53.88%'><img border=0
src="slide0005_image067.png" style='position:absolute;top:46.64%;left:15.76%;
width:15.89%;height:53.35%'><img border=0 src="slide0005_image068.png"
style='position:absolute;top:46.64%;left:80.0%;width:10.99%;height:53.35%'><img
border=0 src="slide0005_image069.png" style='position:absolute;top:41.34%;
left:76.02%;width:11.65%;height:22.79%'><img border=0
src="slide0005_image070.png" style='position:absolute;top:41.51%;left:29.13%;
width:12.71%;height:24.38%'></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>This is a major 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 chromosomes only have a single long arm and the centromere
represents the origin of each chromosome for numerical purpose: 0
centimorgans at almost 0 megabases). The blue labels along the bottom of the
figure list a subset of the 3795 markers that were used in mapping.</font><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 chromosomes summarizes the strength of association between
variation in the phenotype (App expression differences) and the two genotypes
of all 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><font face=Verdana size=3>The red line and the red
axis to the far right provide an estimate of the effect that a QTL has on
expression of App (this estimate of the so-called additive effect tends to be
too high). 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 trait values. Multiply the additive effect
size by 2 to estimate the difference between the set of strains that have the
B/B genotype and those that have the D/D genotype at a specific marker. For
example, on distal Chr 7 the red line peaks at a value of about 0.2. That
means that this region of chromosome 2 is responsible for a 0.4 unit
expression difference between B/B strains and the D/D strains.</font><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 a method to
evaluate 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 using the 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 3 and Chr 7 under the LRS peaks. That
is somewhat reassuring. But notice that a substantial number of bootstrap are
scattered around on other chromosomes. About 30% of the bootstrap resamples
have a peak on Chr 7. That is pretty good, but does makes us realize that the
sample we are working with is still quite small and fragile.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The horizontal dashed
lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values
associated with the suggestive and significant genome-wide probabilities that
were established by permutations of phenotypes across genotypes. We shuffle
randomly 2000 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 17.3. We call that level the 0.05
significance threshold for a whole genome scan. The p = 0.67 point is 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 3 is probably more than just suggestive.</font><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. 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 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 Analysis window
with the genotypes loaded into the window just like any other trait. More on
this in Section 3.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4. You can drag these maps
off of the browser window and onto your desktop. They will be saved as PNG or
PDF files. You can import them into Photoshop or other programs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>5. There is also an option
at the bottom of the page to download a 2X higher resolution image of this
plot for papers and presentations.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>6. You can also download
the results of the analysis in a text format</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/html/webqtl_demo2.ppt_files/slide0005_image013.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image013.png Binary files differdeleted file mode 100755 index 55769e36..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image013.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image014.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image014.png Binary files differdeleted file mode 100755 index e49ba16e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image014.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image066.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image066.png Binary files differdeleted file mode 100755 index 5ab7794c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image066.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image067.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image067.png Binary files differdeleted file mode 100755 index c26d4792..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image067.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image068.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image068.png Binary files differdeleted file mode 100755 index af0745a5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image068.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image069.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image069.png Binary files differdeleted file mode 100755 index 6ec88720..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image069.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image070.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image070.png Binary files differdeleted file mode 100755 index 9c156ddc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image070.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_notes_pane.htm deleted file mode 100755 index 279e38cf..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2.ppt.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 a major 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 chromosomes only have a single long arm and the centromere
represents the origin of each chromosome for numerical purpose: 0
centimorgans at almost 0 megabases). The blue labels along the bottom of the
figure list a subset of the 3795 markers that were used in mapping.</font><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 chromosomes summarizes the strength of association between
variation in the phenotype (App expression differences) and the two genotypes
of all 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><font face=Verdana size=2>The red line and the red
axis to the far right provide an estimate of the effect that a QTL has on
expression of App (this estimate of the so-called additive effect tends to be
too high). 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 trait values. Multiply the additive effect
size by 2 to estimate the difference between the set of strains that have the
B/B genotype and those that have the D/D genotype at a specific marker. For
example, on distal Chr 7 the red line peaks at a value of about 0.2. That
means that this region of chromosome 2 is responsible for a 0.4 unit
expression difference between B/B strains and the D/D strains.</font><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 a method to
evaluate 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 using the 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 3 and Chr 7 under the LRS peaks. That
is somewhat reassuring. But notice that a substantial number of bootstrap are
scattered around on other chromosomes. About 30% of the bootstrap resamples
have a peak on Chr 7. That is pretty good, but does makes us realize that the
sample we are working with is still quite small and fragile.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>The horizontal dashed
lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values
associated with the suggestive and significant genome-wide probabilities that
were established by permutations of phenotypes across genotypes. We shuffle
randomly 2000 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 17.3. We call that level the 0.05
significance threshold for a whole genome scan. The p = 0.67 point is 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 3 is probably more than just suggestive.</font><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. 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 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 Analysis window
with the genotypes loaded into the window just like any other trait. More on
this in Section 3.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>4. You can drag these maps
off of the browser window and onto your desktop. They will be saved as PNG or
PDF files. You can import them into Photoshop or other programs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>5. There is also an option
at the bottom of the page to download a 2X higher resolution image of this
plot for papers and presentations.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>6. You can also download
the results of the analysis in a text format</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006.htm deleted file mode 100755 index f647c55a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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content="Aug-15-05: Genetic versus Physical maps for App expression">
<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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:-.53%;left:1.72%;width:116.02%;height:8.65%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;position:absolute;top:18.36%;left:.79%;width:99.2%;
height:75.51%'><span style='font-family:Verdana;font-size:64%'><i>Genetic
versus Physical maps for App expression</i></span><span style='font-family:
Verdana;font-size:73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</div>
<img border=0 src="slide0006_image071.png" style='position:absolute;top:8.83%;
left:1.72%;width:98.27%;height:39.92%'><img border=0
src="slide0006_image072.png" style='position:absolute;top:35.51%;left:1.85%;
width:98.27%;height:54.06%'>
<div class=O style='position:absolute;top:91.69%;left:5.96%;width:95.23%;
height:7.42%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-size:117%;color:#E9EB5D'><i>The difference between genetic and
physical scale is analogous to measuring the </i></span></span><span
style='position:absolute;top:42.85%;left:0%;width:96.66%'><span
style='font-size:117%;color:#E9EB5D'><i>separation between New York and Boston
in either travel hours or kilometers</i></span><span style='font-size:150%;
color:#E9EB5D'><i>.</i></span><span style='font-size:167%;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=Verdana size=3>The map on the top has an
X-axis scale based on frequency of recombinations events between markers (B
to D transitions, see slide 19 for a color-coded example). These so-called
genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast,
the physical map shown below the genetic map has an X-axis scale based on DNA
length measured in nucleotides or base-pairs. Notice the large difference
between the two maps in the size of Chr 19 (large on the genetic scale but
small on the physical scale).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Also notice the large
difference in the width of the chromosome 7 QTL peak. In mice, recombinations
occur with higher frequency toward the telomeric side (right side) of each
chromosome. As a result, genetic maps are stretched out more toward the
telomere relative to a physical map. The QTL on distal Chr 7 is therefore
actually more precisely mapped than might appear looking at the genetic map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The physical scale is
becoming more useful than the genetic scale primarily because many other data
types can be easily superimposed on a physical map. You will see more
examples in the next several slides.</font><br>
</td>
</tr>
</table>
</div>
<script language=JavaScript><!--
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image015.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image015.png Binary files differdeleted file mode 100755 index ff7d776a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image015.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image071.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image071.png Binary files differdeleted file mode 100755 index 0e63f836..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image071.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image072.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image072.png Binary files differdeleted file mode 100755 index 3c44c2ab..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image072.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_notes_pane.htm deleted file mode 100755 index c1f7d244..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
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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=Verdana size=2>The map on the top has an
X-axis scale based on frequency of recombinations events between markers (B
to D transitions, see slide 19 for a color-coded example). These so-called
genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast,
the physical map shown below the genetic map has an X-axis scale based on DNA
length measured in nucleotides or base-pairs. Notice the large difference
between the two maps in the size of Chr 19 (large on the genetic scale but
small on the physical scale).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Also notice the large
difference in the width of the chromosome 7 QTL peak. In mice, recombinations
occur with higher frequency toward the telomeric side (right side) of each
chromosome. As a result, genetic maps are stretched out more toward the
telomere relative to a physical map. The QTL on distal Chr 7 is therefore
actually more precisely mapped than might appear looking at the genetic map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>The physical scale is
becoming more useful than the genetic scale primarily because many other data
types can be easily superimposed on a physical map. You will see more
examples in the next several slides.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007.htm deleted file mode 100755 index 01fb76a9..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
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mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%;
height:75.51%'><span style='font-family:Verdana;font-size:64%'>Physical map for
distal chromosome 7</span><span style='font-family:Verdana;font-size:73%;
mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</div>
<div style='position:absolute;top:7.77%;left:5.82%;width:94.03%;height:6.18%;
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<div class=O style='position:absolute;top:11.42%;left:1.12%;width:98.87%;
height:74.28%'><span style='font-size:167%;color:#E9EB5D'>Distal Chr 7 from
~120 and 132 Mb may modulate</span><span style='font-size:167%;color:#E9EB5D'><i>
App</i></span><span style='font-size:200%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><i><br>
</i></span></div>
</div>
<img border=0 src="slide0007_image073.png" style='position:absolute;top:93.28%;
left:6.62%;width:75.23%;height:3.71%'><img border=0 src="slide0007_image075.png"
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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>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Physical map of variation
in App expression in brain on distal Chr 7 (a blow up of the whole-genome map
on the previous slide).</font><br>
</td>
</tr>
<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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana
size=3> You can now see that the X-axis is on a physical scale of megabases
(Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. The small irregular
colored blocks and marks toward the top of the map mark the locations of
genes superimposed on the physical map. Neighboring genes are offset slightly
in the vertical axis for display purpose. Note one region of very high gene
density from about 120 to 123 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. The orange hash marks
along the X-axis represent the number of single nucleotide polymorphisms that
distinguish the two parental strains (C57BL/6J and DBA/2J) from each other.
We call this the SNP seismograph track (see Glossary for more details). Regions
with low numbers of SNPs have closely matched sequences and are less likely
to contain QTLs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4. As before, the thin red
line shows the additive effect size. By convention the positive values
signify the D alleles are associated with higher expression of App in this
region of Chr 7 than the B alleles. The maximum effect size is about +0.20
log2 expression units per D allele. The differences been the BB and DD
genotypes (BB and DD because each strain has two alleles; one per chromosome)
is therefore about 2^0.4 = 1.32 or a 32% increment in DD relative to BB at
this locus.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>5. If you scroll just
under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO
YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps
are zoomable, a feature we will exploit to evaluate candidate genes in this
QTL interval.</font><br>
</td>
</tr>
</table>
</div>
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image016.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image016.png Binary files differdeleted file mode 100755 index 53a17c76..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image016.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image017.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image017.png Binary files differdeleted file mode 100755 index 308c4df0..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image017.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image073.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image073.png Binary files differdeleted file mode 100755 index c0174c3f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image073.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image075.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image075.png Binary files differdeleted file mode 100755 index 9a3e3264..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image075.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_notes_pane.htm deleted file mode 100755 index 24c42724..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
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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>Physical map of variation
in App expression in brain on distal Chr 7 (a blow up of the whole-genome map
on the previous slide).</font><br>
</td>
</tr>
<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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana
size=2> You can now see that the X-axis is on a physical scale of megabases
(Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2. The small irregular
colored blocks and marks toward the top of the map mark the locations of
genes superimposed on the physical map. Neighboring genes are offset slightly
in the vertical axis for display purpose. Note one region of very high gene
density from about 120 to 123 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>3. The orange hash marks
along the X-axis represent the number of single nucleotide polymorphisms that
distinguish the two parental strains (C57BL/6J and DBA/2J) from each other.
We call this the SNP seismograph track (see Glossary for more details). Regions
with low numbers of SNPs have closely matched sequences and are less likely
to contain QTLs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>4. As before, the thin red
line shows the additive effect size. By convention the positive values
signify the D alleles are associated with higher expression of App in this
region of Chr 7 than the B alleles. The maximum effect size is about +0.20
log2 expression units per D allele. The differences been the BB and DD
genotypes (BB and DD because each strain has two alleles; one per chromosome)
is therefore about 2^0.4 = 1.32 or a 32% increment in DD relative to BB at
this locus.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>5. If you scroll just
under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO
YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps
are zoomable, a feature we will exploit to evaluate candidate genes in this
QTL interval.</font><br>
</td>
</tr>
</table>
</body>
</html>
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style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img
border=0 src="slide0008_image076.png" style='position:absolute;top:34.09%;
left:1.72%;width:97.48%;height:61.48%'>
<div style='position:absolute;top:-1.06%;left:.79%;width:93.64%;height:8.65%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
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left:1.41%;width:97.31%;height:75.51%'><span style='font-family:Verdana;
font-size:64%'>Evaluating candidate genes</span><span style='font-family:Verdana;
font-size:73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</div>
<img border=0 src="slide0008_image077.png" style='position:absolute;top:8.83%;
left:1.72%;width:34.83%;height:22.61%'>
<div style='position:absolute;top:3.35%;left:69.53%;width:33.9%;height:17.84%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:3.96%;left:2.73%;width:93.75%;
height:91.08%'>
<div style='text-align:center;position:absolute;top:0%;left:0%;width:100.0%;
height:33.69%'><span style='font-size:200%;color:#E9EB5D'><i>Right
position<br>
</i></span></div>
<div style='text-align:center;position:absolute;top:32.6%;left:0%;width:100.0%;
height:67.39%'><span style='position:absolute;top:0%;left:.41%;width:100.0%'><span
style='font-size:200%;color:#E9EB5D'><i>and high </i></span></span><span
style='position:absolute;top:50.0%;left:0%;width:100.0%'><span
style='font-size:200%;color:#E9EB5D'><i>correlation</i></span></span></div>
</div>
</div>
<div style='position:absolute;top:17.84%;left:75.89%;width:21.72%;height:14.31%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:3.7%;left:0%;width:100.0%;height:
88.88%'>
<div style='text-align:center;position:absolute;top:0%;left:6.7%;width:86.58%;
height:58.33%'><span style='font-size:267%;color:#E9EB5D'><i><span
style="mso-spacerun: yes"> </span></i></span><span style='font-size:200%;
color:#E9EB5D'><i>= better<br>
</i></span></div>
<div style='text-align:center;position:absolute;top:56.94%;left:0%;width:100.0%;
height:43.05%'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></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="Times New Roman" size=4><b>Evaluating
candidate genes (CHECKED BOXES) responsible for variability in APP
expression:</b></font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>A large number
of genes are usually in the QTL interval and are therefore POSITIONAL
CANDIDATES, but they will differ greatly in their biological and
bioinformatic plausibility. Assume that the QTL has been located between 119
and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we
might need to evaluate several hundred positional candidates. In this
particular case there are about 100 known genes in this interval. Eight of
these are highlighted in the table above with check marks in the boxes to the
left.<span style="mso-spacerun: yes"> </span>We need to highlight and
objectively score the biologically relevant subset of all 100 positional
candidate genes. We could look through gene ontologies and expression levels
to help us shorten the list. An alternate way available using WebQTL is to
generate a list of those genes in this interval that have transcripts that
co-vary in expression with App expression. That is what the table shows.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate
this table go back to the Trait Data and Analysis Form. Choose to sort
correlations by POSITION and select RETURN = 500. Then scroll down the list
to Chr 7 and review the subset of positional candidates that share expression
with App. You should see a list similar to that shown above. Gtf3c1 is a good
biological candidate and has a high covariation in expression with App.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span
style="mso-spacerun: yes"> </span>Of course, the gene or genes
that control App expression may not be in this list. A protein coding
difference might be the ultimate cause of variation in App transcript level
and the expression covariation might be close to zero. Our list may also
simply be missing the right transcript since the microarray is not truly
comprehensive. Furthermore, even if the list contains the QTL gene, an
expression difference may only have been expressed early in development or
even in another tissue such as liver. While it is important to recognize
these caveats, it is equally important to devise a rational way to rank
candidates given existing data. Coexpression is one of several criteria used
to evaluate positional candidates. We will see others in the next slide.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>3. We can also
assess the likelihood that candidates contain functional polymorphism in
promoters and enhancers that affect their expression simply by mapping the
transcripts of all candidate genes to see if they Òmap backÓ to the location
of gene itself. A transcript that maps to its own location is referred to as
a cis QTL. We essentially ask: Which of the transcripts listed in the
Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression
that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes">
</span>The logic of this search is that if a gene controls the level of its
own expression it is also much more likely to generate other downstream
effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of
about 7.0 (D alleles are high). That is just about sufficient to declare it
to be a cis QTL. [No whole genome correction is required and a point-wise
p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly
equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
</table>
</div>
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<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>Evaluating
candidate genes (CHECKED BOXES) responsible for variability in APP
expression:</b></font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>A large number
of genes are usually in the QTL interval and are therefore POSITIONAL
CANDIDATES, but they will differ greatly in their biological and
bioinformatic plausibility. Assume that the QTL has been located between 119
and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we
might need to evaluate several hundred positional candidates. In this
particular case there are about 100 known genes in this interval. Eight of
these are highlighted in the table above with check marks in the boxes to the
left.<span style="mso-spacerun: yes"> </span>We need to highlight and
objectively score the biologically relevant subset of all 100 positional
candidate genes. We could look through gene ontologies and expression levels
to help us shorten the list. An alternate way available using WebQTL is to
generate a list of those genes in this interval that have transcripts that
co-vary in expression with App expression. That is what the table shows.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate
this table go back to the Trait Data and Analysis Form. Choose to sort
correlations by POSITION and select RETURN = 500. Then scroll down the list
to Chr 7 and review the subset of positional candidates that share expression
with App. You should see a list similar to that shown above. Gtf3c1 is a good
biological candidate and has a high covariation in expression with App.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span
style="mso-spacerun: yes"> </span>Of course, the gene or genes
that control App expression may not be in this list. A protein coding
difference might be the ultimate cause of variation in App transcript level
and the expression covariation might be close to zero. Our list may also
simply be missing the right transcript since the microarray is not truly
comprehensive. Furthermore, even if the list contains the QTL gene, an
expression difference may only have been expressed early in development or
even in another tissue such as liver. While it is important to recognize
these caveats, it is equally important to devise a rational way to rank
candidates given existing data. Coexpression is one of several criteria used
to evaluate positional candidates. We will see others in the next slide.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>3. We can also
assess the likelihood that candidates contain functional polymorphism in
promoters and enhancers that affect their expression simply by mapping the
transcripts of all candidate genes to see if they Òmap backÓ to the location
of gene itself. A transcript that maps to its own location is referred to as
a cis QTL. We essentially ask: Which of the transcripts listed in the
Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression
that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes">
</span>The logic of this search is that if a gene controls the level of its
own expression it is also much more likely to generate other downstream
effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of
about 7.0 (D alleles are high). That is just about sufficient to declare it
to be a cis QTL. [No whole genome correction is required and a point-wise
p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly
equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
</table>
</body>
</html>
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<div style='position:absolute;top:-.53%;left:1.72%;width:101.05%;height:8.65%;
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<div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%;
height:75.51%'><span style='font-family:Verdana;font-size:64%'>Physical maps
are zoomable</span><span style='font-family:Verdana;font-size:73%;mso-special-format:
lastCR;display:none'><i><br>
</i></span></div>
</div>
<img border=0 src="slide0009_image078.png" style='position:absolute;top:8.83%;
left:3.31%;width:89.93%;height:41.69%'><img border=0
src="slide0009_image079.png" style='position:absolute;top:44.52%;left:7.54%;
width:42.91%;height:48.76%'><img border=0 src="slide0009_image080.png"
style='position:absolute;top:94.52%;left:0%;width:97.08%;height:3.71%'></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>An even higher blow-up of
part of the Chr 7 physical map of variation in App expression in brain.<span
style="mso-spacerun: yes"> </span>The QTL region actually extends from
about 119 to 129.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned
in the previous slide another important approach to ranking candidates is
based on the number of sequence variants that distinguish the parental
strains. If we were sure that the sequences of the gene, its promoter, and
its enhancers were identical between the strains then we could discount--but
not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls
into this category: of 663 known SNPs in and around this gene, only four
differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially
identical-by-descent in these strains and is a less likely candidate. In
contrast, if the two alleles of the gene have dozens of functional variants
in exons, promoters, enhancers, and splice sites, then it becomes a higher
priority candidate.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>Of course it
only takes a single critical sequence variant to generate downstream effects.
The argument above is really about the prior probabilities. Where would you
place your bets given the information at hand?</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2.<span
style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL
ANALYST you will find that Ctbp2 is a particularly interesting candidate that
contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is
also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots
of SNPs but it is also is associated with a powerful cis QTL with an LRS of
24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3.<span
style="mso-spacerun: yes"> </span>At this high magnification,
individual genes are distinct. They are color coded by their density of SNPs.
Bright orange represents those genes that have a high SNP density (C57BL/6J
versus DBA/2J), black represents genes with low SNP density. Roll the cursor
over a gene block and its name will pop up, along with information on exon
number.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4.<span
style="mso-spacerun: yes"> </span>Beneath the physical map you will
find an INTERVAL ANALYST table that lists information on known genes in the
region on which you have zoomed the Physical Map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>5.<span
style="mso-spacerun: yes"> </span>As always: error-checking is
important. Some genes may be missing from the Interval Analyst (recent
additions or errors of omission). In this case the Zranb1 gene that is
located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST.
Double-check the interval using the Genome Browser links (blue and beige
horizontal bars) at the top of the PHYSICAL MAP.</font><br>
</td>
</tr>
</table>
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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>An even higher blow-up of
part of the Chr 7 physical map of variation in App expression in brain.<span
style="mso-spacerun: yes"> </span>The QTL region actually extends from
about 119 to 129.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned
in the previous slide another important approach to ranking candidates is
based on the number of sequence variants that distinguish the parental
strains. If we were sure that the sequences of the gene, its promoter, and
its enhancers were identical between the strains then we could discount--but
not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls
into this category: of 663 known SNPs in and around this gene, only four
differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially
identical-by-descent in these strains and is a less likely candidate. In
contrast, if the two alleles of the gene have dozens of functional variants
in exons, promoters, enhancers, and splice sites, then it becomes a higher
priority candidate.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>Of course it
only takes a single critical sequence variant to generate downstream effects.
The argument above is really about the prior probabilities. Where would you
place your bets given the information at hand?</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2.<span
style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL
ANALYST you will find that Ctbp2 is a particularly interesting candidate that
contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is
also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots
of SNPs but it is also is associated with a powerful cis QTL with an LRS of
24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>3.<span
style="mso-spacerun: yes"> </span>At this high magnification,
individual genes are distinct. They are color coded by their density of SNPs.
Bright orange represents those genes that have a high SNP density (C57BL/6J
versus DBA/2J), black represents genes with low SNP density. Roll the cursor
over a gene block and its name will pop up, along with information on exon
number.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>4.<span
style="mso-spacerun: yes"> </span>Beneath the physical map you will
find an INTERVAL ANALYST table that lists information on known genes in the
region on which you have zoomed the Physical Map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>5.<span
style="mso-spacerun: yes"> </span>As always: error-checking is
important. Some genes may be missing from the Interval Analyst (recent
additions or errors of omission). In this case the Zranb1 gene that is
located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST.
Double-check the interval using the Genome Browser links (blue and beige
horizontal bars) at the top of the PHYSICAL MAP.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010.htm deleted file mode 100755 index 91cf9f00..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:0%;left:1.72%;width:106.35%;height:7.24%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;position:absolute;top:12.19%;left:.87%;width:99.12%;
height:90.24%'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span
style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span
style='font-family:Verdana;font-size:64%'> as a candidate QTL for </span><span
style='font-family:Verdana;font-size:64%'><i>App</i></span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
</div>
<img border=0 src="slide0010_image082.png" style='position:absolute;top:94.52%;
left:3.31%;width:96.68%;height:4.24%'><img border=0 src="slide0010_image083.png"
style='position:absolute;top:7.77%;left:3.31%;width:48.34%;height:40.28%'>
<div class=O style='position:absolute;top:52.82%;left:55.23%;width:35.76%;
height:37.98%'><span style='position:absolute;top:0%;left:0%;width:94.81%'><span
style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;
color:#E9EB5D'><i> the </i></span></span><span style='position:absolute;
top:16.74%;left:0%;width:95.92%'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2
</i></span><span style='font-size:233%;color:#E9EB5D'>cis QTL, </span></span><span
style='position:absolute;top:33.48%;left:0%;width:98.14%'><span
style='font-size:233%;color:#E9EB5D'>but is detected </span></span><span
style='position:absolute;top:49.76%;left:0%;width:94.81%'><span
style='font-size:233%;color:#E9EB5D'>only in the </span></span><span
style='position:absolute;top:66.51%;left:0%;width:100.0%'><span
style='font-size:233%;color:#E9EB5D'>Rosen striatum </span></span><span
style='position:absolute;top:83.25%;left:0%;width:94.81%'><span
style='font-size:233%;color:#E9EB5D'>data set.</span><span style='font-size:
233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
<div class=O style='position:absolute;top:16.25%;left:56.02%;width:48.21%;
height:12.72%'><span style='position:absolute;top:0%;left:0%;width:94.78%'><span
style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;
color:#E9EB5D'><i> the App QTL </i></span></span><span style='position:absolute;
top:48.61%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'>in
the INIA data set. </span><span style='font-size:233%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><i><br>
</i></span></span></div>
<img border=0 src="slide0010_image084.png" style='position:absolute;top:39.39%;
left:3.31%;width:48.47%;height:53.35%'><img border=0
src="slide0010_image085.png" style='position:absolute;top:10.95%;left:35.36%;
width:.39%;height:72.79%'><img border=0 src="slide0010_image086.png"
style='position:absolute;top:10.95%;left:31.52%;width:.39%;height:72.79%'></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 slide illustrates one
reason why Ctbp2 should be considered a high priority positional candidate
gene that may modulate the expression level of App.<span style="mso-spacerun:
yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the
data are taken from the striatum).<span style="mso-spacerun: yes">
</span>If Ctbp2 contains variants that modulate its own expression then these
expression differences may produce many downstream effects. Of course, we now
want to know much more about the known biology of Ctbp2. What kind of gene is
it? To begin to answer that question we can use a number of resources listed
in the LINKS page.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana
size=3> The App QTL is bimodal. Perhaps there are actually two causal factors
in this region--one close to 123 Mb and the other close to 127 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. The precision of QTL
mapping depends on several factors, including the effect size and
interactions among QTLs modulating a trait, the number of genetic individuals
that are studied, and the distribution of recombinations in the study
population.<span style="mso-spacerun: yes"> </span>In the case above,
the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The
bootstrap test (yellow bars shown in some of the previous slides) can be
usual for estimating the consistency of QTL peaks.</font><br>
</td>
</tr>
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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>This slide illustrates one
reason why Ctbp2 should be considered a high priority positional candidate
gene that may modulate the expression level of App.<span style="mso-spacerun:
yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the
data are taken from the striatum).<span style="mso-spacerun: yes">
</span>If Ctbp2 contains variants that modulate its own expression then these
expression differences may produce many downstream effects. Of course, we now
want to know much more about the known biology of Ctbp2. What kind of gene is
it? To begin to answer that question we can use a number of resources listed
in the LINKS page.</font><br>
</td>
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<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=Verdana size=2>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana
size=2> The App QTL is bimodal. Perhaps there are actually two causal factors
in this region--one close to 123 Mb and the other close to 127 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2. The precision of QTL
mapping depends on several factors, including the effect size and
interactions among QTLs modulating a trait, the number of genetic individuals
that are studied, and the distribution of recombinations in the study
population.<span style="mso-spacerun: yes"> </span>In the case above,
the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The
bootstrap test (yellow bars shown in some of the previous slides) can be
usual for estimating the consistency of QTL peaks.</font><br>
</td>
</tr>
</table>
</body>
</html>
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visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:0%;left:1.72%;width:101.05%;height:8.65%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%;
height:75.51%'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span
style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span
style='font-family:Verdana;font-size:64%'> using other resources</span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
</div>
<img border=0 src="slide0011_image087.png" style='position:absolute;top:10.07%;
left:1.72%;width:48.21%;height:53.35%'><img border=0
src="slide0011_image088.png" style='position:absolute;top:40.81%;left:19.2%;
width:78.54%;height:54.77%'></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=Verdana size=3>Ctbp2 should also be
considered a high priority biological candidate gene responsible for
modulating App expression levels. The C-terminal binding protein 2 is a
transcriptional co-repressor also known as Ribeye.</font><font
face=Times-Roman size=3> The gene produces two transcripts encoding distinct
proteins. The short form is a transcriptional repressor that binds a
Pro-X-Asp-Leu-Ser peptide motif and interacts with several transcription
factors including EVI1, ZFPM1, and ZFHX1A (aka TCF8, deltaEF1). The longer
isoform is a major component of specialized synapses in photoreceptors. Both
proteins contain a NAD+ binding domain similar to NAD+-dependent
2-hydroxyacid dehydrogenases.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>1. To find out more about
CTBP2 protein and the Ctbp2 gene, link to iHOP at
http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Try Arrowsmith at
http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. Both APP and CTBP2 are
involved in oxidoreducatase activity or Notch signaling. To establish this
common gene ontology visit NCBI<span style="mso-spacerun: yes">
</span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene and enter each gene
symbol.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. You can get interesting
hints regarding Ctbp2 expression partners by examining the genetic
correlations between Ctbp2 probe set 1422887_a_at and all other transcripts
on the M430 Affymetrix array. Use the Striatum data set because we already
know from previous work (the previous slide) that this gene is a cis
QTL.<span style="mso-spacerun: yes"> </span>You should be able to show
that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The
negative genetic correlation with E2f4 is even stronger. The transcript also
has a high positive genetic correlation with Rdh14. Of particular interest
with respect to APP protein processing, Ctbp2 covaries positively with Bace2
(the transcript of the beta site APP-cleaving enzyme 2).</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><br>
</td>
</tr>
</table>
</div>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
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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>Ctbp2 should also be
considered a high priority biological candidate gene responsible for
modulating App expression levels. The C-terminal binding protein 2 is a
transcriptional co-repressor also known as Ribeye.</font><font
face=Times-Roman size=2> The gene produces two transcripts encoding distinct
proteins. The short form is a transcriptional repressor that binds a
Pro-X-Asp-Leu-Ser peptide motif and interacts with several transcription
factors including EVI1, ZFPM1, and ZFHX1A (aka TCF8, deltaEF1). The longer
isoform is a major component of specialized synapses in photoreceptors. Both
proteins contain a NAD+ binding domain similar to NAD+-dependent
2-hydroxyacid dehydrogenases.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>1. To find out more about
CTBP2 protein and the Ctbp2 gene, link to iHOP at
http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Try Arrowsmith at
http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2. Both APP and CTBP2 are
involved in oxidoreducatase activity or Notch signaling. To establish this
common gene ontology visit NCBI<span style="mso-spacerun: yes">
</span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene and enter each gene
symbol.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>3. You can get interesting
hints regarding Ctbp2 expression partners by examining the genetic
correlations between Ctbp2 probe set 1422887_a_at and all other transcripts
on the M430 Affymetrix array. Use the Striatum data set because we already
know from previous work (the previous slide) that this gene is a cis
QTL.<span style="mso-spacerun: yes"> </span>You should be able to show
that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The
negative genetic correlation with E2f4 is even stronger. The transcript also
has a high positive genetic correlation with Rdh14. Of particular interest
with respect to APP protein processing, Ctbp2 covaries positively with Bace2
(the transcript of the beta site APP-cleaving enzyme 2).</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><br>
</td>
</tr>
</table>
</body>
</html>
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visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:-.35%;left:3.31%;width:93.64%;height:14.48%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292;
mso-text-indent-alt:0;position:absolute;top:0%;left:1.13%;width:97.59%;
height:51.21%'><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'>Summary of Part 2</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:15.01%;left:5.96%;width:101.19%;height:31.09%'>
<div class=O1 style='mso-margin-left-alt:432'></div>
<div class=O2 style='mso-margin-left-alt:720'></div>
<div class=O3 style='mso-margin-left-alt:1008'></div>
<div class=O4 style='mso-margin-left-alt:1296'></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:0%;
left:0%;width:86.25%;height:14.2%'><span style='position:absolute;top:0%;
left:2.88%;width:97.11%'><span style='font-family:"Gill Sans";font-size:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.96%;font-family:Arial'>1.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Covered the basics of QTL
analysis and mapping.<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:14.2%;
left:0%;width:86.25%;height:14.2%'><span style='position:absolute;top:0%;
left:2.88%;width:97.11%'><span style='font-family:"Gill Sans";font-size:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.96%;font-family:Arial'>2.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Reviewed difference between
genetic and physical maps.<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:28.4%;
left:0%;width:100.0%;height:42.61%'><span style='position:absolute;top:0%;
left:2.48%;width:97.51%'><span style='font-family:"Gill Sans";font-size:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.55%;font-family:Arial'>3.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Discussed interpreting features
of QTL maps including the LRS function, </span></span><span style='position:
absolute;top:33.33%;left:2.48%;width:91.23%'><span style='font-family:"Gill Sans";
font-size:167%;color:#E9EB5D;mso-color-index:3'>the additive effect function,
the bootstrap bars, and the permutation </span></span><span style='position:
absolute;top:68.0%;left:2.48%;width:83.76%'><span style='font-family:"Gill Sans";
font-size:167%;color:#E9EB5D;mso-color-index:3'>thresholds.<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:71.59%;
left:0%;width:88.35%;height:14.2%'><span style='position:absolute;top:0%;
left:2.81%;width:97.18%'><span style='font-family:"Gill Sans";font-size:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.89%;font-family:Arial'>4.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Illustrated techniques to
generate a list of positional candidates.<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:85.79%;
left:0%;width:86.25%;height:14.2%'><span style='position:absolute;top:0%;
left:2.88%;width:97.11%'><span style='font-family:"Gill Sans";font-size:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.96%;font-family:Arial'>5.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Discussed some factors used to
evaluate candidate genes.</span></span></div>
</div>
<div class=O style='position:absolute;top:58.65%;left:5.96%;width:106.22%;
height:22.26%'><span style='position:absolute;top:0%;left:0%;width:84.53%'><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'>What does a QTL signify? A good QTL is a claim that a particular </span></span><span
style='position:absolute;top:19.84%;left:0%;width:96.38%'><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'>chromosomal region contains a causal source of variation in the phenotype. </span></span><span
style='position:absolute;top:39.68%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'>The importance of this hypothesis depends on the quality and relevance of
the </span></span><span style='position:absolute;top:59.52%;left:0%;width:90.89%'><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'>phenotype and the statistical strength of the QTL. As usual, test and be </span></span><span
style='position:absolute;top:79.36%;left:0%;width:84.53%'><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'>skeptical.</span></span></div>
</div>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
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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=Helvetica size=2>By clicking on the
CORRELATION of the Atcay transcript to the App transcript, you can generate a
Correlation plot between these two transcripts. In this App and Atcay
scatterplot, each point is a strain mean value. For example, BXD33 and BXD8
have low App and Atcay expressions. The two parental strains and the F1 are
also included in this plot.</font><br>
</td>
</tr>
</table>
</body>
</html>
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style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:0%;left:1.72%;width:101.05%;height:8.65%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%;
height:75.51%'><span style='font-family:Verdana;font-size:64%'>Test Questions</span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
</div>
<div class=O style='position:absolute;top:11.83%;left:4.37%;width:108.34%;
height:6.53%'><span style='font-size:233%;color:#E9EB5D'>1. Evaluate candidates
for the Chr 3 </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span
style='font-size:233%;color:#E9EB5D'> QTL.</span><span style='font-size:233%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
<div class=O style='position:absolute;top:24.02%;left:4.9%;width:100.92%;
height:12.72%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-size:233%;color:#E9EB5D'>2. Do </span><span style='font-size:233%;
color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> and
</span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span
style='font-size:233%;color:#E9EB5D'> expression share any </span></span><span
style='position:absolute;top:50.0%;left:0%;width:93.43%'><span
style='font-size:233%;color:#E9EB5D'>other QTLs beside that on Chr 7?</span><span
style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
<div class=O style='position:absolute;top:43.99%;left:4.9%;width:102.91%;
height:19.08%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-size:233%;color:#E9EB5D'>3. Can you exploit literature mining tools
to </span></span><span style='position:absolute;top:33.33%;left:0%;width:98.45%'><span
style='font-size:233%;color:#E9EB5D'>find a strong relationship between </span><span
style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:
233%;color:#E9EB5D'> and </span></span><span style='position:absolute;
top:65.74%;left:0%;width:91.63%'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span
style='font-size:233%;color:#E9EB5D'>? </span><span style='font-size:233%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
<div class=O style='position:absolute;top:69.08%;left:4.9%;width:110.19%;
height:12.72%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-size:233%;color:#E9EB5D'>4. Why might the cis QTL for </span><span
style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:
233%;color:#E9EB5D'> expression </span></span><span style='position:absolute;
top:50.0%;left:0%;width:89.66%'><span style='font-size:233%;color:#E9EB5D'>only
be detected in the striatum data set?</span><span style='font-size:233%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></div>
</div>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
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href="webqtl_demo2.ppt.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>A group of traits from
many different databases can be selected and brought together for joint
analysis. In this case all of the content of the BXD SELECTIONS is from a
single BRAIN database, the top 20 neighbors of the App transcript from the
Correlation Results table. Eight of these neighbors plus App is shown in the
slide.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font
face=Helvetica size=2>All of items in the BXD SELECTIONS were selected using
the SELECT ALL button</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>2. The buttons at the
top (and bottom) of this page can do some cool stuff. We will work with
NETWORK GRAPH first.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>3. Think of the
SELECTIONS as your shopping cart. You go to different aisles in the
supermarket to acquire different types of items of interest. These could
include transcripts, classical phenotypes (longevity, brain weight, prepulse
inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves
doing some analysis with the items in the cart.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>4. Different tools
handle different numbers of items. Most will handle up to 100 traits.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
</table>
</body>
</html>
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style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:2.29%;left:2.51%;width:94.43%;height:9.89%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:19.64%;
left:1.4%;width:97.47%;height:69.64%'><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:16.6%;left:6.62%;width:90.19%;height:24.38%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:0%;
left:1.46%;width:97.35%;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:34.05%;left:4.67%;width:95.47%'><span
style='font-size:82%'><br>
</span></span><span style='position:absolute;
top:68.11%;left:4.67%;width:95.47%'><span style='font-size:82%;mso-special-format:
lastCR;display:none'><br>
</span></span></div>
</div>
<div class=O style='position:absolute;top:27.56%;left:9.4%;width:50.59%;
height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'>kmanly@utmem.edu</span></div>
<div class=O style='position:absolute;top:83.56%;left:4.37%;width:108.34%;
height:15.9%'><span style='position:absolute;top:0%;left:0%;width:90.83%'><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'>The </span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'><i>App</i></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'> findings reviewed
in this presentation are part of an </span></span><span style='position:absolute;
top:33.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";
font-size:200%;color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and
R. Clark (July 15, </span></span><span style='position:absolute;top:66.66%;
left:0%;width:84.35%'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D'>2005)</span><span style='font-family:"Gill Sans";font-size:300%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><br>
</span></span></div>
</div>
<div id=NotesObj style='display:none'>
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<td width=5 nowrap></td>
<td width="100%"></td>
</tr>
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<td align=left colspan=1><font face=Verdana size=3>END</font><br>
</td>
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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;
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mso-text-raise:0%;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232;
mso-text-indent-alt:0;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232;
mso-text-indent-alt:0'><script> - mytop = 0 * 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-size:73%'>The GeneNetwork and WebQTL
: PART 2<span style="mso-spacerun: yes"> </span><br>
</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:73%'>link to www.genenetwork.org</span><span
style='font-size:73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></layer></div>
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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:94%;color:#E9EB5D;mso-color-index:3'>Part 1. How to study </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * 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'>expression variation </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.47 * 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'>and genetic correlation </span></span></layer><script> - mytop = 0.15 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * 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'>(slides 2–17)<br>
</span></span></layer></div>
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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
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style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
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style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'>(slides 18–29)</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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17'><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>
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mso-special-format:lastCR;display:none'><br>
</span></div>
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<div></div>
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<div><script language=JavaScript><!--
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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>
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<tr>
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<td align=left colspan=1><font face=Helvetica size=3>Part 2: Discovering
upstream modulators and quantitative trait loci (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>
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<tr>
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<td align=left colspan=1><font face=Helvetica size=2>Going back to the Trait
Data and Analysis Form window, we have computed the correlations between
strain variation in App expression level and other classical phenotypes that
have already been measured in many of the same BXD strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font
face=Helvetica size=2>The number of common strains varies widely--in this
case from 14 to 23 strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>2. We can add these
traits (four are selected) to our BXD SELECTIONS window.</font><br>
</td>
</tr>
</table>
</body>
</html>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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style='font-family:Arial;font-size:150%;color:aqua;display:none'><br>
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</span></div>
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</layer></div>
</layer><script> - mytop = 0.28 * g_height; myleft = 0.45 * g_width; myheight = 0.01 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.45 * g_width; -yy = 0.28 * g_height; -ht = 0.01 * g_height; -wd = 0.18 * g_width; -document.write( -'<img border=0 src="slide0002_image003.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.2 * g_height; myleft = 0.28 * 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 = 0.28 * g_width; -yy = 0.2 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image004.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.15 * g_height; myleft = 0.25 * g_width; myheight = 0.09 * g_height; mywidth = 0.19 * 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 = 0.18 * 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 = 0.03 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>C57BL/6J
(B)<br>
</span></div>
</layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 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 = 0.2 * g_height; myleft = 0.3 * 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 = 0.3 * g_width; -yy = 0.2 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image005.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.15 * g_height; myleft = 0.62 * g_width; myheight = 0.09 * g_height; mywidth = 0.16 * 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 = 0.15 * 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 = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J
(D)<br>
</span></div>
</layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 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 = 0.2 * g_height; myleft = 0.66 * 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 = 0.66 * g_width; -yy = 0.2 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image006.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.23 * g_width; myheight = 0.01 * g_height; mywidth = 0.5 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.23 * g_width; -yy = 0.35 * g_height; -ht = 0.01 * g_height; -wd = 0.5 * g_width; -document.write( -'<img border=0 src="slide0002_image007.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.24 * 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 = 0.24 * g_width; -yy = 0.35 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image008.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.4 * 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 = 0.4 * g_width; -yy = 0.35 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image009.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.57 * 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 = 0.57 * g_width; -yy = 0.35 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image010.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.74 * 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 = 0.74 * g_width; -yy = 0.35 * g_height; -ht = 0.03 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image011.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.42 * g_height; myleft = 0.05 * 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 = 0.01 * 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:"-230 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:"-230 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="slide0002_image012.png" 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="slide0002_image013.png" 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="slide0002_image014.png" 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="slide0002_image015.png" 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="slide0002_image016.png" 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="slide0002_image017.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.71 * g_height; myleft = 0.58 * g_width; myheight = 0.26 * 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:"-269 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:"-269 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="slide0002_image018.png" 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="slide0002_image019.png" 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="slide0002_image020.png" 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="slide0002_image021.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.92 * g_height; myleft = 0.21 * g_width; myheight = 0.09 * 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:"-173 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:"-173 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 = 0.09 * 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:"-173 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:"-173 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 = 0.05 * 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:"-173 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:"-173 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:"-341 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:"-341 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:"-230 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:"-230 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="slide0002_image022.png" 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="slide0002_image023.png" 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="slide0002_image024.png" 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="slide0002_image025.png" 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="slide0002_image026.png" 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="slide0002_image027.png" 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="slide0002_image028.png" 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="slide0002_image029.png" 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="slide0002_image030.png" 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="slide0002_image031.png" 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="slide0002_image032.png" 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="slide0002_image033.png" 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="slide0002_image034.png" 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="slide0002_image035.png" 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="slide0002_image036.png" 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="slide0002_image037.png" 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="slide0002_image038.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.75 * g_height; myleft = 0.01 * g_width; myheight = 0.13 * g_height; mywidth = 0.13 * 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:"-173 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:"-173 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:"-173 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="slide0002_image039.png" 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="slide0002_image040.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.2 * g_height; myleft = 0.17 * g_width; myheight = 0.13 * 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:"-173 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:"-173 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:"-173 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 = 0.09 * g_height; mywidth = 0.11 * 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:"-173 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:"-173 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 = 0.13 * 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:"-173 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:"-173 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:"-173 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 = 0.21 * g_height; mywidth = 0.21 * 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:"-173 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:"-173 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 = 0.09 * 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:"-173 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:"-173 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 = 0.09 * g_height; mywidth = 0.07 * 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:"-173 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:"-173 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 = 0.3 * g_height; myleft = 0.78 * g_width; myheight = 0.09 * g_height; mywidth = 0.19 * 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 = 0.07 * 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 = 0.03 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><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>
</layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 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 = 0.31 * g_height; myleft = 0.65 * g_width; myheight = 0.02 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.65 * g_width; -yy = 0.31 * g_height; -ht = 0.02 * g_height; -wd = 0.12 * g_width; -document.write( -'<img border=0 src="slide0002_image041.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.86 * g_height; myleft = 0.03 * 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 * g_height; myleft = 0 * g_width; myheight = 0.12 * 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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%;
color:#E9EB5D'>Inbred<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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%;
color:#E9EB5D'>Isogenic<br>
</span></div>
</layer><script> - mytop = 0.06 * 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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><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>
</layer><script> - mytop = 0.09 * 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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%;
color:aqua;mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.79 * g_height; myleft = 0.83 * 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 = 0.83 * g_width; -yy = 0.79 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image042.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.84 * g_height; myleft = 0.83 * 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 = 0.83 * g_width; -yy = 0.84 * g_height; -ht = 0.02 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image043.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.79 * g_height; myleft = 0.53 * 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 = 0.53 * g_width; -yy = 0.79 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image044.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.83 * g_height; myleft = 0.53 * 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 = 0.53 * g_width; -yy = 0.83 * g_height; -ht = 0.01 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image045.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.8 * g_height; myleft = 0.23 * 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 = 0.23 * g_width; -yy = 0.8 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image046.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.18 * g_height; myleft = 0.43 * g_width; myheight = 0.09 * g_height; mywidth = 0.13 * 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 = 0.07 * g_height; mywidth = 0.12 * 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:"-341 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17'><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>
</layer></div>
</layer><script> - mytop = 0.27 * g_height; myleft = 0.32 * g_width; myheight = 0.04 * g_height; mywidth = 0.31 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.32 * g_width; -yy = 0.27 * g_height; -ht = 0.04 * g_height; -wd = 0.31 * g_width; -document.write( -'<img border=0 src="slide0002_image047.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.66 * g_height; myleft = 0.6 * g_width; myheight = 0.03 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.6 * g_width; -yy = 0.66 * g_height; -ht = 0.03 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image048.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.64 * g_height; myleft = 0.15 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.15 * g_width; -yy = 0.64 * g_height; -ht = 0.05 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image049.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.75 * g_width; -yy = 0.57 * g_height; -ht = 0.05 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image050.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.28 * g_height; myleft = 0.48 * g_width; myheight = 0.08 * 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 = 0.28 * g_height; -ht = 0.08 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image051.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.62 * g_height; myleft = 0.23 * g_width; myheight = 0.16 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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<td align=left colspan=1><font face=Verdana size=3>The next few slides
provide a short introduction to mapping the loci that are responsible for
variation in a trait such as App expression level. These modulatory regions
of the genome are sometimes called quantitative trait loci or QTLs. You may
want to do some independent reading on this topic if this is your first
exposure to QTL analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The genetic reference
population (GRP) of BXD recombinant inbred strains were originally generated
about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed
female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2
progeny. At the bottom of this slide we have schematized one chromosome pair
from three of the BXD RI strains.<span style="mso-spacerun: yes">
</span>The dashed vertical lines that lead to the final BXD RI lines involve
21 full sib matings (about 7 years of breeding). Some lines die out during
inbreeding. For example, there is no longer any BXD3 strain.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>1. Over the last decade,
our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at
Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD
strains. They have all been genotyped using about 13,700 markers (SNPs and
microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ
regions of the chromosomes as shown in the figure above.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. Chromosomes of RI GRPs
usually have about 4 times as many recombinations as those of F2 animals.
However, unlike an F2, both chromosomes of an RI are identical. Therefore,
50 RI strains contain as many recombinations as 100 F2 animals.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. BXD43 through BXD100
were generated using a special method that resulted in a further doubling of
the average recombination density per chromosome. The entire set of 80 BXDs
therefore contains as many recombinations as about 260 F2 animals.</font><br>
</td>
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<head>
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<td width="100%"></td>
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<td align=left colspan=1><font face=Helvetica size=2>We have computed the
Network Graph, now using other types of traits.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Saline Hot Plate Latency
is the green node labeled 10020.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Freezing (fear) is the
green node labeled 10447.</font><br>
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<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
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<div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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<div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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<div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
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</span></div>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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</span></div>
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<div style='mso-line-spacing:"-422 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>
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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:
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<div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
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<div style='mso-line-spacing:"-384 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:"-384 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:"-384 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="slide0003_image058.png" 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:"-350 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:"-350 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:"-350 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:"-350 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 = 0.79 * g_height; myleft = 0.05 * g_width; myheight = 0.13 * g_height; mywidth = 1.04 * 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 = 0.12 * g_height; mywidth = 1.02 * 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:"-256 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:"-256 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 = 1.02 * 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 = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 1.02 * 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'>.</span></span></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:"-233 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:"-233 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:"-233 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 = 0.17 * g_height; mywidth = 0.16 * 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:"-350 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:"-350 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 = 0.17 * 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:"-350 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:"-350 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 = 0.17 * g_height; mywidth = 0.05 * 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:"-350 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:"-350 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></div>
</layer><script> - mytop = 0.71 * g_height; myleft = 0.07 * g_width; myheight = 0.12 * g_height; mywidth = 0.16 * 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 = 0.14 * 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 = 0.05 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span
style='font-size:200%;color:#E9EB5D;display:none'><br>
</span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-233 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></div>
</layer><script> - mytop = 0.57 * g_height; myleft = -0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = -0.01 * g_width; -yy = 0.57 * g_height; -ht = 0.07 * g_height; -wd = 1.01 * g_width; -document.write( -'<img border=0 src="slide0003_image059.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.44 * g_height; myleft = 0.47 * g_width; myheight = 0.12 * 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 = 0.06 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:233%;color:#F6BF69'>Low<br>
</span></div>
</layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.58 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.13 * 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 = 0.04 * g_height; mywidth = 1.12 * 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:"-200 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:"-200 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>
</layer></div>
</layer><script> - mytop = 0.37 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.08 * g_width; -yy = 0.37 * g_height; -ht = 0.2 * g_height; -wd = 0.13 * g_width; -document.write( -'<img border=0 src="slide0003_image060.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.4 * g_height; myleft = 0.1 * 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 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 = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
font-size:233%;color:white'><b></b></span><span style='font-family:Palatino;
font-size:233%;color:white;display:none'><b><br>
</b></span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%;
color:white;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</layer></div>
</layer><script> - mytop = 0.4 * g_height; myleft = 0.18 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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<div style='mso-line-spacing:"-233 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 align=left colspan=1><font face=Helvetica size=3>This slide is
illustrates two major types of QTLs that modulate variability in
transcript-relative steady state abundance.</font><br>
</td>
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<td align=left colspan=1><br>
</td>
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<td align=left colspan=1><font face=Helvetica size=3>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 binding of a
transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms
in enhancers or may be in 3Õ UTR binding sites that affect message
stability.</font><br>
</td>
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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=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 fairly 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 overlapping
arrows in the figure.<span style="mso-spacerun: yes"> </span>The way
in which an upstream polymorphism influences a downstream difference in mRNA
abundance can be indirect. Effects can:</font><br>
</td>
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<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>
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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>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>
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mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span
style='font-family:Verdana;font-size:64%'>Discovering upstream modulatory loci</span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
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<td width="100%"></td>
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<td align=left colspan=1><font face=Verdana size=3>Please bring the Trait
Data and Analysis window to the front and look for the Interval Mapping
button. 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>
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<td align=left colspan=1><br>
</td>
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<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 Mapping Scale is
set to GENETIC</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Options: Permutation test
YES<span style="mso-spacerun: yes"> </span>(2000 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 (2000 is the default number)</font><br>
</td>
</tr>
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<td align=left colspan=1><font face=Helvetica size=2>Part 2: Discovering
upstream modulators and quantitative trait loci (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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mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>WebQTL
searches for upstream controllers</i></span><span style='font-family:Verdana;
font-size:73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
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style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>App maps
on Chr 16 (blue </i></span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.44 * 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:167%;color:#E9EB5D'><i>triangle)
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style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>locus is
on Chr 7.</i></span><span style='font-size:233%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><i><br>
</i></span></span></layer></div>
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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=Verdana size=3>This is a major 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 chromosomes only have a single long arm and the centromere
represents the origin of each chromosome for numerical purpose: 0
centimorgans at almost 0 megabases). The blue labels along the bottom of the
figure list a subset of the 3795 markers that were used in mapping.</font><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 chromosomes summarizes the strength of association between
variation in the phenotype (App expression differences) and the two
genotypes of all 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><font face=Verdana size=3>The red line and the red
axis to the far right provide an estimate of the effect that a QTL has on
expression of App (this estimate of the so-called additive effect tends to
be too high). 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 trait values. Multiply the
additive effect size by 2 to estimate the difference between the set of
strains that have the B/B genotype and those that have the D/D genotype at a
specific marker. For example, on distal Chr 7 the red line peaks at a value
of about 0.2. That means that this region of chromosome 2 is responsible for
a 0.4 unit expression difference between B/B strains and the D/D strains.</font><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 a
method to evaluate 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 using the 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 3 and Chr 7 under the LRS peaks. That
is somewhat reassuring. But notice that a substantial number of bootstrap
are scattered around on other chromosomes. About 30% of the bootstrap
resamples have a peak on Chr 7. That is pretty good, but does makes us
realize that the sample we are working with is still quite small and
fragile.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The horizontal dashed
lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values
associated with the suggestive and significant genome-wide probabilities
that were established by permutations of phenotypes across genotypes. We
shuffle randomly 2000 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 17.3. We call that level
the 0.05 significance threshold for a whole genome scan. The p = 0.67 point
is 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 3 is probably more than just suggestive.</font><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. 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 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 Analysis window
with the genotypes loaded into the window just like any other trait. More on
this in Section 3.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4. You can drag these
maps off of the browser window and onto your desktop. They will be saved as
PNG or PDF files. You can import them into Photoshop or other programs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>5. There is also an
option at the bottom of the page to download a 2X higher resolution image of
this plot for papers and presentations.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>6. You can also download
the results of the analysis in a text format</font><br>
</td>
</tr>
</table>
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<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.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="100%"></td>
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<td align=left colspan=1><font face=Verdana size=2>The next few slides
provide a short introduction to mapping the loci that are responsible for
variation in a trait such as App expression level. These modulatory regions
of the genome are sometimes called quantitative trait loci or QTLs. You may
want to do some independent reading on this topic if this is your first
exposure to QTL analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>The genetic reference
population (GRP) of BXD recombinant inbred strains were originally generated
about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed
female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny.
At the bottom of this slide we have schematized one chromosome pair from
three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The
dashed vertical lines that lead to the final BXD RI lines involve 21 full sib
matings (about 7 years of breeding). Some lines die out during inbreeding.
For example, there is no longer any BXD3 strain.</font><br>
</td>
</tr>
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<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Notes:</font><br>
</td>
</tr>
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<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>1. Over the last decade,
our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at
Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD
strains. They have all been genotyped using about 13,700 markers (SNPs and
microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ
regions of the chromosomes as shown in the figure above.</font><br>
</td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2. Chromosomes of RI GRPs
usually have about 4 times as many recombinations as those of F2 animals.
However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50
RI strains contain as many recombinations as 100 F2 animals.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>3. BXD43 through BXD100
were generated using a special method that resulted in a further doubling of
the average recombination density per chromosome. The entire set of 80 BXDs
therefore contains as many recombinations as about 260 F2 animals.</font><br>
</td>
</tr>
</table>
</body>
</html>
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mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>Genetic
versus Physical maps for App expression</i></span><span style='font-family:
Verdana;font-size:73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
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style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>The
difference between genetic and physical scale is analogous to measuring the </i></span></span></layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>separation
between New York and Boston in either travel hours or kilometers</i></span><span
style='font-size:150%;color:#E9EB5D'><i>.</i></span><span style='font-size:
167%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</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>The map on the top has an
X-axis scale based on frequency of recombinations events between markers (B
to D transitions, see slide 19 for a color-coded example). These so-called
genetic maps are scaled in centimorgan (recombinations per 100 gametes). In
contrast, the physical map shown below the genetic map has an X-axis scale
based on DNA length measured in nucleotides or base-pairs. Notice the large
difference between the two maps in the size of Chr 19 (large on the genetic
scale but small on the physical scale).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Also notice the large
difference in the width of the chromosome 7 QTL peak. In mice,
recombinations occur with higher frequency toward the telomeric side (right
side) of each chromosome. As a result, genetic maps are stretched out more
toward the telomere relative to a physical map. The QTL on distal Chr 7 is
therefore actually more precisely mapped than might appear looking at the
genetic map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The physical scale is
becoming more useful than the genetic scale primarily because many other
data types can be easily superimposed on a physical map. You will see more
examples in the next several slides.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
-</script><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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2.ppt.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 major types of QTLs that modulate variability in
transcript-relative steady state 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 binding of a
transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms
in enhancers or may be in 3Õ UTR binding sites that affect message stability.</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 fairly 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 overlapping
arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in
which an upstream polymorphism influences a downstream difference in mRNA
abundance can be 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>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm deleted file mode 100755 index c7854145..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm +++ /dev/null @@ -1,110 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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<meta name=Description content="Aug-15-05: Physical map for distal chromosome 7">
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<div><script language=JavaScript><!--
-ht = g_height; -wd = g_width; -document.write( -'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); -//-->
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<div><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * 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:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Physical
map for distal chromosome 7</span><span style='font-family:Verdana;font-size:
73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</layer></div>
</layer><script> - mytop = 0.07 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * 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 = 0.04 * 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: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:167%;color:#E9EB5D'>Distal Chr 7 from
~120 and 132 Mb may modulate</span><span style='font-size:167%;color:#E9EB5D'><i>
App</i></span><span style='font-size:200%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><i><br>
</i></span></div>
</layer></div>
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-</script></div>
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-</script></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>Physical map of variation
in App expression in brain on distal Chr 7 (a blow up of the whole-genome
map on the previous slide).</font><br>
</td>
</tr>
<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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Verdana size=3> You can now see that the X-axis is on a physical scale
of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. The small irregular
colored blocks and marks toward the top of the map mark the locations of
genes superimposed on the physical map. Neighboring genes are offset
slightly in the vertical axis for display purpose. Note one region of very
high gene density from about 120 to 123 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. The orange hash marks
along the X-axis represent the number of single nucleotide polymorphisms
that distinguish the two parental strains (C57BL/6J and DBA/2J) from each
other. We call this the SNP seismograph track (see Glossary for more
details). Regions with low numbers of SNPs have closely matched sequences
and are less likely to contain QTLs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4. As before, the thin
red line shows the additive effect size. By convention the positive values
signify the D alleles are associated with higher expression of App in this
region of Chr 7 than the B alleles. The maximum effect size is about +0.20
log2 expression units per D allele. The differences been the BB and DD
genotypes (BB and DD because each strain has two alleles; one per
chromosome) is therefore about 2^0.4 = 1.32 or a 32% increment in DD
relative to BB at this locus.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>5. If you scroll just
under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO
YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps
are zoomable, a feature we will exploit to evaluate candidate genes in this
QTL interval.</font><br>
</td>
</tr>
</table>
</div>
</layer>
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-//-->
-</script><script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2.ppt.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>Please bring the Trait
Data and Analysis window to the front and look for the Interval Mapping
button. 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 Mapping Scale is
set to GENETIC</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Options: Permutation test
YES<span style="mso-spacerun: yes"> </span>(2000 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 (2000 is the default number)</font><br>
</td>
</tr>
</table>
</body>
</html>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span
style='font-family:Verdana;font-size:64%'>Evaluating candidate genes</span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
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<div><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.31 * 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 = 0.31 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>Right
position<br>
</i></span></div>
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<div style='text-align:center'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.31 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>and
high </i></span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.31 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>correlation</i></span></span></layer></div>
</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%'><script> - mytop = 0 * g_height; myleft = 0.01 * 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='text-align:center'><span style='font-size:267%;color:#E9EB5D'><i><span
style="mso-spacerun: yes"> </span></i></span><span style='font-size:200%;
color:#E9EB5D'><i>= better<br>
</i></span></div>
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<div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></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="Times New Roman" size=4><b>Evaluating
candidate genes (CHECKED BOXES) responsible for variability in APP
expression:</b></font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>A large number
of genes are usually in the QTL interval and are therefore POSITIONAL
CANDIDATES, but they will differ greatly in their biological and
bioinformatic plausibility. Assume that the QTL has been located between 119
and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we
might need to evaluate several hundred positional candidates. In this
particular case there are about 100 known genes in this interval. Eight of
these are highlighted in the table above with check marks in the boxes to
the left.<span style="mso-spacerun: yes"> </span>We need to highlight
and objectively score the biologically relevant subset of all 100 positional
candidate genes. We could look through gene ontologies and expression levels
to help us shorten the list. An alternate way available using WebQTL is to
generate a list of those genes in this interval that have transcripts that
co-vary in expression with App expression. That is what the table shows.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate
this table go back to the Trait Data and Analysis Form. Choose to sort
correlations by POSITION and select RETURN = 500. Then scroll down the list
to Chr 7 and review the subset of positional candidates that share
expression with App. You should see a list similar to that shown above.
Gtf3c1 is a good biological candidate and has a high covariation in
expression with App.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span
style="mso-spacerun: yes"> </span>Of course, the gene or genes
that control App expression may not be in this list. A protein coding
difference might be the ultimate cause of variation in App transcript level
and the expression covariation might be close to zero. Our list may also
simply be missing the right transcript since the microarray is not truly
comprehensive. Furthermore, even if the list contains the QTL gene, an
expression difference may only have been expressed early in development or
even in another tissue such as liver. While it is important to recognize
these caveats, it is equally important to devise a rational way to rank
candidates given existing data. Coexpression is one of several criteria used
to evaluate positional candidates. We will see others in the next slide.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>3. We can also
assess the likelihood that candidates contain functional polymorphism in
promoters and enhancers that affect their expression simply by mapping the
transcripts of all candidate genes to see if they Òmap backÓ to the location
of gene itself. A transcript that maps to its own location is referred to as
a cis QTL. We essentially ask: Which of the transcripts listed in the
Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression
that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes">
</span>The logic of this search is that if a gene controls the level of its
own expression it is also much more likely to generate other downstream
effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of
about 7.0 (D alleles are high). That is just about sufficient to declare it
to be a cis QTL. [No whole genome correction is required and a point-wise
p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly
equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
</table>
</div>
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<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 a major 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 chromosomes only have a single long arm and the centromere
represents the origin of each chromosome for numerical purpose: 0
centimorgans at almost 0 megabases). The blue labels along the bottom of the
figure list a subset of the 3795 markers that were used in mapping.</font><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 chromosomes summarizes the strength of association between
variation in the phenotype (App expression differences) and the two genotypes
of all 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><font face=Verdana size=2>The red line and the red
axis to the far right provides an estimate of the effect that a QTL has on
expression of App (this estimate of the so-called additive effect tends to be
too high). 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 trait values. Multiply the additive effect
size by 2 to estimate the difference between the set of strains that have the
B/B genotype and those that have the D/D genotype at a specific marker. For
example, on distal Chr 7 the red line peaks at a value of about 0.2. That
means that this region of chromosome 2 is responsible for a 0.4 unit
expression difference between B/B strains and the D/D strains.</font><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 a method to
evaluate 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 using the 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 3 and Chr 7 under the LRS peaks. That
is somewhat reassuring. But notice that a substantial number of bootstrap are
scattered around on other chromosomes. About 30% of the bootstrap resamples
have a peak on Chr 7. That is pretty good, but does makes us realize that the
sample we are working with is still quite small and fragile.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>The horizontal dashed
lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values
associated with the suggestive and significant genome-wide probabilities that
were established by permutations of phenotypes across genotypes. We shuffle
randomly 2000 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 17.3. 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 3 is probably more than just suggestive.</font><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. 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 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 Analysis window
with the genotypes loaded into the window just like any other trait. More on
this in Section 3.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>4. You can drag these maps
off of the browser window and onto your desktop. They will be saved as PNG or
PDF files. You can import them into Photoshop or other programs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>5. There is also an option
at the bottom of the page to download a 2X higher resolution image of this
plot for papers and presentations.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>6. You can also download
the results of the analysis in a text format</font><br>
</td>
</tr>
</table>
</body>
</html>
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font-style:normal;text-decoration:none;text-shadow:none;text-effect:none;
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mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Physical
maps are zoomable</span><span style='font-family:Verdana;font-size:73%;
mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
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<div><script language=JavaScript><!--
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</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>An even higher blow-up of
part of the Chr 7 physical map of variation in App expression in brain.<span
style="mso-spacerun: yes"> </span>The QTL region actually extends from
about 119 to 129.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned
in the previous slide another important approach to ranking candidates is
based on the number of sequence variants that distinguish the parental
strains. If we were sure that the sequences of the gene, its promoter, and
its enhancers were identical between the strains then we could discount--but
not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls
into this category: of 663 known SNPs in and around this gene, only four
differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially
identical-by-descent in these strains and is a less likely candidate. In
contrast, if the two alleles of the gene have dozens of functional variants
in exons, promoters, enhancers, and splice sites, then it becomes a higher
priority candidate.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>Of course it
only takes a single critical sequence variant to generate downstream
effects. The argument above is really about the prior probabilities. Where
would you place your bets given the information at hand?</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2.<span
style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL
ANALYST you will find that Ctbp2 is a particularly interesting candidate
that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2
is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain
lots of SNPs but it is also is associated with a powerful cis QTL with an
LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3.<span
style="mso-spacerun: yes"> </span>At this high magnification,
individual genes are distinct. They are color coded by their density of
SNPs. Bright orange represents those genes that have a high SNP density
(C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll
the cursor over a gene block and its name will pop up, along with
information on exon number.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4.<span
style="mso-spacerun: yes"> </span>Beneath the physical map you will
find an INTERVAL ANALYST table that lists information on known genes in the
region on which you have zoomed the Physical Map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>5.<span
style="mso-spacerun: yes"> </span>As always: error-checking is
important. Some genes may be missing from the Interval Analyst (recent
additions or errors of omission). In this case the Zranb1 gene that is
located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST.
Double-check the interval using the Genome Browser links (blue and beige
horizontal bars) at the top of the PHYSICAL MAP.</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/html/webqtl_demo2.ppt_files/slide0023_image107.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image107.png Binary files differdeleted file mode 100755 index 0e63f836..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image107.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image108.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image108.png Binary files differdeleted file mode 100755 index 3c44c2ab..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image108.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_notes_pane.htm deleted file mode 100755 index 010f3332..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm">
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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=Verdana size=2>The map on the top has an
X-axis scale based on frequency of recombinations events between markers (B
to D transitions, see slide 19 for a color-coded example). These so-called
genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast,
the physical map shown below the genetic map has an X-axis scale based on DNA
length measured in nucleotides or base-pairs. Notice the large difference
between the two maps in the size of Chr 19 (large on the genetic scale but
small on the physical scale).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Also notice the large
difference in the width of the chromosome 7 QTL peak. In mice, recombinations
occur with higher frequency toward the telomeric side (righ sidet) of each
chromosome. As a result, genetic maps are stretched out more toward the
telomere relative to a physical map. The QTL on distal Chr 7 is therefore
actually more precisely mapped than might appear looking at the genetic map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>The physical scale is
becoming more useful than the genetic scale primarily because many other data
types can be easily superimposed on a physical map. You will see more
examples in the next several slides.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024.htm deleted file mode 100755 index bf2b9b3c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024.htm +++ /dev/null @@ -1,167 +0,0 @@ -<html>
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content="Aug-15-05: Evaluating Ctbp2 as a candidate QTL for App">
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<div><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.05 * 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:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Evaluating
</span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span
style='font-family:Verdana;font-size:64%'> as a candidate QTL for </span><span
style='font-family:Verdana;font-size:64%'><i>App</i></span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
</layer></div>
</layer><script> - mytop = 0.94 * g_height; myleft = 0.03 * g_width; myheight = 0.04 * g_height; mywidth = 0.96 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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<div><script language=JavaScript><!--
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</layer><script> - mytop = 0.52 * g_height; myleft = 0.55 * g_width; myheight = 0.37 * g_height; mywidth = 0.35 * 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 = 0.33 * 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'>This is</span><span
style='font-size:233%;color:#E9EB5D'><i> the </i></span></span></layer><script> - mytop = 0.06 * 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-size:233%;color:#E9EB5D'><i>Ctbp2 </i></span><span
style='font-size:233%;color:#E9EB5D'>cis QTL, </span></span></layer><script> - mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * 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'>but is
detected </span></span></layer><script> - mytop = 0.18 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * 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'>only in the </span></span></layer><script> - mytop = 0.25 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * 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'>Rosen
striatum </span></span></layer><script> - mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * 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'>data set.</span><span
style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></layer></div>
</layer><script> - mytop = 0.16 * g_height; myleft = 0.56 * g_width; myheight = 0.12 * g_height; mywidth = 0.48 * 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 = 0.45 * 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'>This is</span><span
style='font-size:233%;color:#E9EB5D'><i> the App QTL </i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.48 * 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'>in the INIA
data set. </span><span style='font-size:233%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><i><br>
</i></span></span></layer></div>
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<td align=left colspan=1><font face=Verdana size=3>This slide illustrates
one reason why Ctbp2 should be considered a high priority positional
candidate gene that may modulate the expression level of App.<span
style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some
brain regions (here the data are taken from the striatum).<span
style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that
modulate its own expression then these expression differences may produce
many downstream effects. Of course, we now want to know much more about the
known biology of Ctbp2. What kind of gene is it? To begin to answer that
question we can use a number of resources listed in the LINKS page.</font><br>
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<td align=left colspan=1><br>
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<td align=left colspan=1><font face=Verdana size=3>Notes:</font><br>
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<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Verdana size=3> The App QTL is bimodal. Perhaps there are actually two
causal factors in this region--one close to 123 Mb and the other close to
127 Mb.</font><br>
</td>
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<td align=left colspan=1><font face=Verdana size=3>2. The precision of QTL
mapping depends on several factors, including the effect size and
interactions among QTLs modulating a trait, the number of genetic
individuals that are studied, and the distribution of recombinations in the
study population.<span style="mso-spacerun: yes"> </span>In the case
above, the QTL(s) are likely to be confined to the interval from 120 to 132
Mb. The bootstrap test (yellow bars shown in some of the previous slides)
can be usual for estimating the consistency of QTL peaks.</font><br>
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<td align=left colspan=1><font face=Verdana size=2>Physical map of variation
in App expression in brain on distal Chr 7 (a blow up of the whole-genome map
on the previous slide).</font><br>
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<td align=left colspan=1><font face=Verdana size=2>Notes:</font><br>
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<td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana
size=2> You can now see that the X-axis is on a physical scale of megabases
(Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br>
</td>
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<td align=left colspan=1><font face=Verdana size=2>2. The small irregular
colored blocks and marks toward the top of the map mark the locations of
genes superimposed on the physical map. Neighboring genes are offset slightly
in the vertical axis for display purpose. Note one region of very high gene
density from about 120 to 123 Mb.</font><br>
</td>
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<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>3. The orange hash marks
along the X-axis represent the number of single nucleotide polymorphisms that
distinguish the two parental strains (C57BL/6J and DBA/2J) from each other.
We call this the SNP seismograph track (see Glossary for more details). Regions
with low numbers of SNP have closely matched sequences and are less likely to
contain QTLs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>4. As before, the thin red
line shows the additive effect size. By convention the positive values
signify the D alleles are associated with higher expression of App in this
region of Chr 7 than the B alleles. The maximum effect size is about +0.20
log2 expression units per D allele. The differences been the BB and DD
genotypes (BB and DD because each strain has two alleles; one per chromosome)
is therefore about 2^0.4 = 1.32; or a 32% increment in DD relative to BB at
this locus.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>5. If you scroll just
under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO
YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps
are zoomable, a feature we will exploit to evaluate candidate genes in this
QTL interval.</font><br>
</td>
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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;
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mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Evaluating
</span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span
style='font-family:Verdana;font-size:64%'> using other resources</span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
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<td align=left colspan=1><font face=Verdana size=3>Ctbp2 should also be
considered a high priority biological candidate gene responsible for
modulating App expression levels. The C-terminal binding protein 2 is a
transcriptional co-repressor also known as Ribeye.</font><font
face=Times-Roman size=3> The gene produces two transcripts encoding distinct
proteins. The short form is a transcriptional repressor that binds a
Pro-X-Asp-Leu-Ser peptide motif and interacts with several transcription
factors including EVI1, ZFPM1, and ZFHX1A (aka TCF8, deltaEF1). The longer
isoform is a major component of specialized synapses in photoreceptors. Both
proteins contain a NAD+ binding domain similar to NAD+-dependent
2-hydroxyacid dehydrogenases.</font><br>
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<td align=left colspan=1><font face=Verdana size=3>Notes:</font><br>
</td>
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<td align=left colspan=1><font face=Verdana size=3>1. To find out more about
CTBP2 protein and the Ctbp2 gene, link to iHOP at
http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Try Arrowsmith at
http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. Both APP and CTBP2 are
involved in oxidoreducatase activity or Notch signaling. To establish this
common gene ontology visit NCBI<span style="mso-spacerun: yes">
</span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene and enter each gene
symbol.</font><br>
</td>
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<td align=left colspan=1><font face=Verdana size=3>3. You can get
interesting hints regarding Ctbp2 expression partners by examining the
genetic correlations between Ctbp2 probe set 1422887_a_at and all other
transcripts on the M430 Affymetrix array. Use the Striatum data set because
we already know from previous work (the previous slide) that this gene is a
cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to
show that Ctbp2 and Notch3 have antagonistic expression patterns in
striatum. The negative genetic correlation with E2f4 is even stronger. The
transcript also has a high positive genetic correlation with Rdh14. Of
particular interest with respect to APP protein processing, Ctbp2 covaries
positively with Bace2 (the transcript of the beta site APP-cleaving enzyme
2).</font><br>
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<td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating
candidate genes (CHECKED BOXES) responsible for variability in APP
expression:</b></font><br>
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<td align=left colspan=1><font face="Times New Roman" size=4>A large number
of genes are usually in the QTL interval and are therefore POSITIONAL
CANDIDATES, but they will differ greatly in their biological and
bioinformatic plausibility. Assume that the QTL has been located between 119
and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we
might need to evaluate several hundred positional candidates. In this
particular case there are about 100 known genes in this interval. Eight of
these are highlighted in the table above with check marks in the boxes to the
left.<span style="mso-spacerun: yes"> </span>We need to highlight and
objectively score the biologically relevant subset of all 100 positional
candidate genes. We could look through gene ontologies and expression levels
to help us shorten the list. An alternate way available using WebQTL is to
generate a list of those genes in this interval that have transcripts that
co-vary in expression with App expression. That is what the table shows.</font><br>
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<td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br>
</td>
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<td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate
this table go back to the Trait Data and Analysis Form. Choose to sort
correlations by POSITION and select RETURN = 500. Then scroll down the list
to Chr 7 and review the subset of positional candidates that share expression
with App. You should see a list similar to that shown above. Gtf3c1 is a good
biological candidate and has a high covariation in expression with App.</font><br>
</td>
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<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span
style="mso-spacerun: yes"> </span>Of course, the gene or genes
that control App expression may not be in this list. A protein coding
difference might be the ultimate cause of variation in App transcript level
and the expression covariation might be close to zero. Our list may also
simply be missing the right transcript since the microarray is not truly
comprehensive. Furthermore, even if the list contains the QT gene, an
expression difference may only have been expressed early in development or
even in another tissue such as liver. While it is important to recognize
these caveats, it is equally important to devise a rational way to rank
candidates given existing data. Coexpression is one of several criteria used
to evaluate positional candidates. We will see others in the next slide.</font><br>
</td>
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<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>3. We can also
assess the likelihood that candidates contain functional polymorphism in
promoters and enhancers that affect their expression simply by mapping the
transcripts of all candidate genes to see if they Òmap backÓ to the location
of gene itself. A transcript that maps to its own location is referred to as
a cis QTL. We essentially ask: Which of the the transcripts listed in the
Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression
that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes">
</span>The logic of this search is that if a gene controls the level of its
own expression it is also much more likely to generate other downstream
effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of
about 7.0 (D alleles are high). That is just about sufficient to declare it
to be a cis QTL. [No whole genome correction is required and a point-wise
p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly
equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br>
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<div style='mso-special-format:nobullet;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%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
292;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'>Summary of Part 2</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
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<layer>
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<layer>
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<layer>
<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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mso-text-raise:0%'></div>
</layer>
<script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * 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:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.96%;font-family:Arial'>1.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Covered the basics of QTL
analysis and mapping.<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * 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:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.96%;font-family:Arial'>2.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Reviewed difference between
genetic and physical maps.<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.98 * 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:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.55%;font-family:Arial'>3.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Discussed interpreting features
of QTL maps including the LRS function, </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * 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:167%;
color:#E9EB5D;mso-color-index:3'>the additive effect function, the bootstrap
bars, and the permutation </span></span></layer><script> - mytop = 0.09 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * 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:167%;
color:#E9EB5D;mso-color-index:3'>thresholds.<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.86 * 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:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.89%;font-family:Arial'>4.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Illustrated techniques to
generate a list of positional candidates.<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * 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:167%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.96%;font-family:Arial'>5.</span></span><span
style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Discussed some factors used to
evaluate candidate genes.</span></span></layer></div>
</layer></div>
</layer><script> - mytop = 0.58 * g_height; myleft = 0.05 * g_width; myheight = 0.22 * g_height; mywidth = 1.06 * 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 = 0.04 * 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-family:"Gill Sans";font-size:167%;
color:#E9EB5D;mso-color-index:3'>What does a QTL signify? A good QTL is a claim
that a particular </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.02 * 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:167%;
color:#E9EB5D;mso-color-index:3'>chromosomal region contains a causal source of
variation in the phenotype. </span></span></layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.06 * 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:167%;
color:#E9EB5D;mso-color-index:3'>The importance of this hypothesis depends on
the quality and relevance of the </span></span></layer><script> - mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.96 * 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:167%;
color:#E9EB5D;mso-color-index:3'>phenotype and the statistical strength of the
QTL. As usual, test and be </span></span></layer><script> - mytop = 0.17 * g_height; myleft = 0 * g_width; myheight = 0.04 * 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-family:"Gill Sans";font-size:167%;
color:#E9EB5D;mso-color-index:3'>skeptical.</span></span></layer></div>
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image114.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image114.png Binary files differdeleted file mode 100755 index 93d21c90..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image114.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image115.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image115.png Binary files differdeleted file mode 100755 index fdc27d23..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image115.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image116.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image116.png Binary files differdeleted file mode 100755 index d2cb5ee3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image116.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_notes_pane.htm deleted file mode 100755 index d335b732..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
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<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>Even higher blow-up of
part of the Chr 7 physical map of variation in App expression in brain.<span
style="mso-spacerun: yes"> </span>The QTL region actually extends from
about 119 to 129.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
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<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned
in the previous slide another important approach to ranking candidates is
based on the number of sequence variants that distinguish the parental
strains. If we were sure that the sequences of the gene, its promoter, and
its enhancers were identical between the strains then we could discount--but
not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls
into this category: of 663 known SNPs in and around this gene, only four
differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially
identical-by-descent in these strains and is a less likely candidate. In
contrast, if the two alleles of the gene have dozens of functional variants
in exons, promoters, enhancers, and splice sites, then it becomes a higher
priority candidate.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>Of course it
only takes a single critical sequence variant to generate downstream effects.
The argument above is really about the prior probabilities. Where would you
place your bets given the information at hand?</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2.<span
style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL
ANALYST you will find that Ctbp2 is a particularly interesting candidate that
contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is
also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots
of SNPs but it is also is associated with a powerful cis QTL with an LRS of
24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>3.<span
style="mso-spacerun: yes"> </span>At this high magnification,
individual genes are distinct. They are color coded by their density of SNPs.
Bright orange represents those genes that have a high SNP density (C57BL/6J
versus DBA/2J), black represents genes with low SNP density. Roll the cursor
over a gene block and its name will pop up, along with information on exon
number.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>4.<span
style="mso-spacerun: yes"> </span>Beneath the physical map you will
find an INTERVAL ANALYST table that lists information on known genes in the
region on which you have zoomed the Physical Map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>5.<span
style="mso-spacerun: yes"> </span>As always: error-checking is
important. Some genes may be missing from the Interval Analyst (recent
additions or errors of omission). In this case the Zranb1 gene that is
located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST.
Double-check the interval using the Genome Browser links (blue and beige
horizontal bars) at the top of the PHYSICAL MAP.</font><br>
</td>
</tr>
</table>
</body>
</html>
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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:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Test
Questions</span><span style='font-family:Verdana;font-size:73%;mso-special-format:
lastCR;display:none'><i><br>
</i></span></div>
</layer></div>
</layer><script> - mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 1.08 * 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%'><span style='font-size:233%;color:#E9EB5D'>1. Evaluate
candidates for the Chr 3 </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span
style='font-size:233%;color:#E9EB5D'> QTL.</span><span style='font-size:233%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</layer><script> - mytop = 0.24 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1 * 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 = 1 * 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'>2. Do </span><span
style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:
233%;color:#E9EB5D'> and </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span
style='font-size:233%;color:#E9EB5D'> expression share any </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-size:233%;color:#E9EB5D'>other QTLs
beside that on Chr 7?</span><span style='font-size:233%;color:#E9EB5D;
mso-special-format:lastCR;display:none'><i><br>
</i></span></span></layer></div>
</layer><script> - mytop = 0.43 * g_height; myleft = 0.04 * g_width; myheight = 0.19 * g_height; mywidth = 1.02 * 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 = 1.02 * 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'>3. Can you
exploit literature mining tools to </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.01 * 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'>find a
strong relationship between </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span
style='font-size:233%;color:#E9EB5D'> and </span></span></layer><script> - mytop = 0.12 * 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-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span
style='font-size:233%;color:#E9EB5D'>? </span><span style='font-size:233%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></layer></div>
</layer><script> - mytop = 0.69 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1.1 * 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 = 1.1 * 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'>4. Why might
the cis QTL for </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span
style='font-size:233%;color:#E9EB5D'> expression </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * 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'>only be
detected in the striatum data set?</span><span style='font-size:233%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></layer></div>
</layer></div>
</LAYER>
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image118.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image118.png Binary files differdeleted file mode 100755 index cf5f70f7..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image118.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image119.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image119.png Binary files differdeleted file mode 100755 index a5886d21..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image119.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image120.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image120.png Binary files differdeleted file mode 100755 index 7eb77319..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image120.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image121.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image121.png Binary files differdeleted file mode 100755 index 99f4d04d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image121.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image122.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image122.png Binary files differdeleted file mode 100755 index ac87ce02..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image122.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_notes_pane.htm deleted file mode 100755 index 26d15c0e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2.ppt.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=Verdana size=2>This slide illustrates one
reason why Ctbp2 should be considered a high priority positional candidate
gene that may modulate the expression level of App.<span style="mso-spacerun:
yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the
data are taken from the striatum).<span style="mso-spacerun: yes">
</span>If Ctbp2 contains variants that modulate its own expression then these
expression differencess may produce many downstream effects. Of course, we
now want to know much more about the known biology of Ctbp2. What kind of
gene is it? To begin to answer that question we can use a number of resources
listed in the LINKS page.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana
size=2> The App QTL is bimodal. Perhaps there are actually two causal factors
in this region--one close to 123 Mb and the other close to 127 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2. The precision of QTL
mapping depends on several factors, including the effect size and
interactions among QTLs modulating a trait, the number of genetic individuals
that are studied, and the distribution of recombinations in the study
population.<span style="mso-spacerun: yes"> </span>In the case above,
the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The
bootstrap test (yellow bars shown in some of the previous slides) can be
usual for estimating the consiistency of QTL peaks.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028.htm deleted file mode 100755 index 67711e7c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028.htm +++ /dev/null @@ -1,112 +0,0 @@ -<html>
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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;
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mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><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>
</layer></div>
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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:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * 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:82%'>rwilliam@nb.utmem.edu<br>
</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 = 0.16 * 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
style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR;
display:none'><br>
</span></span></layer></div>
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</layer><script> - mytop = 0.27 * g_height; myleft = 0.09 * g_width; myheight = 0.07 * g_height; mywidth = 0.5 * 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%'><span style='font-family:"Gill Sans";font-size:300%;
color:#E9EB5D'>kmanly@utmem.edu</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%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * 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:200%;
color:#E9EB5D'>The </span><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D'><i>App</i></span><span style='font-family:"Gill Sans";
font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part
of an </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:200%;
color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and R. Clark (July
15, </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * 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:200%;
color:#E9EB5D'>2005)</span><span style='font-family:"Gill Sans";font-size:300%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><br>
</span></span></layer></div>
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<td align=left colspan=1><font face=Verdana size=3>END</font><br>
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<body bgcolor=black text=white>
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<td align=left colspan=1><font face=Verdana size=2>Ctbp2 should also be
considered a high priority biological candidate gene responsible for
modulating App expression levels. The<span style="mso-spacerun: yes">
</span>C-terminal binding protein 2 is a transcriptional co-repressor also
known as Ribeye.</font><font face=Times-Roman size=2> The gene produces two
transcripts encoding distinct proteins. The short form is a transcriptional
repressor that binds a Pro-X-Asp-Leu-Ser peptide motif common to adenoviral
oncoprotein E1a and a related motif in BKLF. This short form also interacts<span
style="mso-spacerun: yes"> </span>with several transcription factors
including EVI1, ZFPM1, and<span style="mso-spacerun: yes">
</span>ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component
of specialized synapses in photoreceptors. Both proteins contain a NAD+
binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br>
</td>
</tr>
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<td colspan=1></td>
<td align=left colspan=1><br>
</td>
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<td align=left colspan=1><font face=Verdana size=2>Notes:</font><br>
</td>
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<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>1. To find out more about
CTBP2 protein and the Ctbp2 gene, link to iHOP at
http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>Try Arrowsmith at
http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>2. Both APP and CTBP2 are
involved in oxidoreducatase activity or Notch signalling. To estabilish this
common gene ontology visit NCBI<span style="mso-spacerun: yes">
</span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span
style="mso-spacerun: yes"> </span>and enter each gene symbol.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=2>3. You can get intersting
hints regarding Ctbp2 expression partners by examining the genetic
correlations between Ctbp2 probe set 1422887_a_at and all other transcripts
on the M430 Affymetrix array. Use the Striatum data set because we already
know from previous work (the previous slide) that this gene is a cis
QTL.<span style="mso-spacerun: yes"> </span>You should be able to show
that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The
negative genetic correlation with E2f4 is even stronger. The transcript also
has a high positive genetic correlation with Rdh14. Of particualr interest
with respect to APP protein processing, Ctbp2 covaries positiviely with Bace2
(the transcript of the beta site APP-cleaving enzyme 2).</font><br>
</td>
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<td align=left colspan=1><br>
</td>
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<td align=left colspan=1><br>
</td>
</tr>
</table>
</body>
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style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>Atcay</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript scatterplot </span></div>
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<td align=left colspan=1><font face=Helvetica size=3>By clicking on the
CORRELATION of the Atcay transcript to the App transcript, you can generate
a Correlation plot between these two transcripts. In this App and Atcay
scatterplot, each point is a strain mean value. For example, BXD33 and BXD8
have low App and Atcay expressions. The two parental strains and the F1 are
also included in this plot.</font><br>
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its neighbors</span></div>
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<td align=left colspan=1><font face=Helvetica size=3>A group of traits from
many different databases can be selected and brought together for joint
analysis. In this case all of the content of the BXD SELECTIONS is from a
single BRAIN database, the top 20 neighbors of the App transcript from the
Correlation Results table. Eight of these neighbors plus App is shown in the
slide.</font><br>
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<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
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<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>All of items in the BXD SELECTIONS were selected using
the SELECT ALL button</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. The buttons at the
top (and bottom) of this page can do some cool stuff. We will work with
NETWORK GRAPH first.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. Think of the
SELECTIONS as your shopping cart. You go to different aisles in the
supermarket to acquire different types of items of interest. These could
include transcripts, classical phenotypes (longevity, brain weight, prepulse
inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves
doing some analysis with the items in the cart.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>4. Different tools
handle different numbers of items. Most will handle up to 100 traits.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><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/html/webqtl_demo2.ppt_files/slide0045.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0045.htm deleted file mode 100755 index 4e705866..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0045.htm +++ /dev/null @@ -1,118 +0,0 @@ -<html>
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mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%;
mso-text-raise:0%'><span style='font-size:82%'><i>App</i></span><span
style='font-size:82%'> transcript coexpression neighborhood</span><span
style='mso-special-format:lastCR;display:none'><br>
</span></div>
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<div><script language=JavaScript><!--
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-</script></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>Output of the Network
Graph. Warm colors (orange and red) are positive correlations above 0.5
whereas cool colors (green and blue) are negative correlations. Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3> All of the nodes (gene/transcripts) on this graph are
clickable.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. For this graph the
App expression values have ÒrevertedÓ to their pre-Windsorized values.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. To generate this
graph, we used the default setting:<span style="mso-spacerun: yes">
</span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use
curved lines (aka ÒedgesÓ).</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/html/webqtl_demo2.ppt_files/slide0046.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm deleted file mode 100755 index 93429543..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm +++ /dev/null @@ -1,104 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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<div style='mso-special-format:nobullet;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%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
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none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Correlations of </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'> with classical traits</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
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<layer>
<div id=NotesObj style='display:none'>
<table style='color:white' border=0 width="100%">
<tr>
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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>Going back to the Trait
Data and Analysis Form window, we have computed the correlations between
strain variation in App expression level and other classical phenotypes that
have already been measured in many of the same BXD strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>The number of common strains varies widely--in this
case from 14 to 23 strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. We can add these
traits (four are selected) to our BXD SELECTIONS window.</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/html/webqtl_demo2.ppt_files/slide0047.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm deleted file mode 100755 index e7568e44..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html>
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<div style='mso-special-format:nobullet;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%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
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none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Network Graph of </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'> with classical traits</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
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<div><script language=JavaScript><!--
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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>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>We have computed the
Network Graph, now using other types of traits.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Saline Hot Plate
Latency is the green node labeled 10020.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Freezing (fear) is the
green node labeled 10447.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
-</script><script language=JavaScript><!--
-function playList() { - -} -//-->
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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292;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'>Summary of Part 1:</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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;
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color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
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style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You have learned the basics
about searching for traits<br>
</span></span></layer></div>
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color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
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style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know some methods to check
data quality<br>
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text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;
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color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-3.03%;font-family:Arial'>3.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to edit bad or
suspicious data<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.85%;font-family:Arial'>4.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to review the
basic statistics of a trait<br>
</span></span></layer></div>
</layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.74%;font-family:Arial'>5.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to generate a
scattergram between two </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * 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:200%;
color:#E9EB5D;mso-color-index:3'>traits using the Traits Correlation tool<br>
</span></span></layer></div>
</layer><script> - mytop = 0.31 * 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>
<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.56%;font-family:Arial'>6.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to add items to
your SELECTIONS window<br>
</span></span></layer></div>
</layer><script> - mytop = 0.37 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.97 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.57%;font-family:Arial'>7.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to generate a
Network Graph of traits that </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * 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:200%;
color:#E9EB5D;mso-color-index:3'>co-vary. </span></span></layer></div>
</layer></div>
</layer><script> - mytop = 0.67 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.05 * 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 = 1.05 * 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:200%;
color:#E9EB5D;mso-color-index:3'>What does genetic covariance mean? The genetic
covariance can </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * 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:200%;
color:#E9EB5D;mso-color-index:3'>be functional and mechanistic, but it can also
be due to linkage </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * 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:200%;
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sampling error or poor </span></span></layer><script> - mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.92 * 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:200%;
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plausibility of </span></span></layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * 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-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'>correlations. Test and be skeptical.</span></span></layer></div>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
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<div><script> - mytop = 0.02 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 0.94 * 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;
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mso-text-indent-alt:0;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232;
mso-text-indent-alt:0'><script> - mytop = 0 * 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-size:73%'>The GeneNetwork and WebQTL
: PART 2<span style="mso-spacerun: yes"> </span><br>
</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:73%'>link to www.genenetwork.org</span><span
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</i></span></span></layer></div>
</layer></div>
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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:94%;color:#E9EB5D;mso-color-index:3'>Part 1. How to study </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * 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'>(slides 2–17)<br>
</span></span></layer></div>
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color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index:
3'>(slides 18–29)</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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style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E;
display:none'><br>
</span></div>
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mso-special-format:lastCR;display:none'><br>
</span></div>
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<div><script language=JavaScript><!--
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<td align=left colspan=1><font face=Helvetica size=3>Part 2: Discovering
upstream modulators and quantitative trait loci (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>
</layer>
<script language=JavaScript><!--
-//-->
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</body>
</html>
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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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(B)<br>
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-</script></div>
</layer><script> - mytop = 0.15 * g_height; myleft = 0.62 * g_width; myheight = 0.09 * g_height; mywidth = 0.16 * 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 = 0.15 * 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 = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J
(D)<br>
</span></div>
</layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 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 = 0.2 * g_height; myleft = 0.66 * 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 = 0.66 * g_width; -yy = 0.2 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0019_image042.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.23 * g_width; myheight = 0.01 * g_height; mywidth = 0.5 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.23 * g_width; -yy = 0.35 * g_height; -ht = 0.01 * g_height; -wd = 0.5 * g_width; -document.write( -'<img border=0 src="slide0019_image043.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.24 * 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 = 0.24 * g_width; -yy = 0.35 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0019_image044.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.4 * 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 = 0.4 * g_width; -yy = 0.35 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0019_image045.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.57 * 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 = 0.57 * g_width; -yy = 0.35 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0019_image046.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.35 * g_height; myleft = 0.74 * 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 = 0.74 * g_width; -yy = 0.35 * g_height; -ht = 0.03 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0019_image047.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.42 * g_height; myleft = 0.05 * 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 = 0.01 * 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:"-230 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:"-230 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="slide0019_image048.png" 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="slide0019_image049.png" 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="slide0019_image050.png" 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="slide0019_image051.png" 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="slide0019_image052.png" 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="slide0019_image053.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.71 * g_height; myleft = 0.58 * g_width; myheight = 0.26 * 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:"-269 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:"-269 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="slide0019_image054.png" 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="slide0019_image055.png" 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="slide0019_image056.png" 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="slide0019_image057.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.92 * g_height; myleft = 0.21 * g_width; myheight = 0.09 * 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:"-173 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:"-173 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 = 0.09 * 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:"-173 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:"-173 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 = 0.05 * 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:"-173 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:"-173 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:"-341 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:"-341 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:"-230 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:"-230 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="slide0019_image058.png" 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="slide0019_image059.png" 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="slide0019_image060.png" 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="slide0019_image061.png" 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="slide0019_image062.png" 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="slide0019_image063.png" 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="slide0019_image064.png" 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="slide0019_image065.png" 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="slide0019_image066.png" 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="slide0019_image067.png" 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="slide0019_image068.png" 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="slide0019_image069.png" 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="slide0019_image070.png" 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="slide0019_image071.png" 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="slide0019_image072.png" 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="slide0019_image073.png" 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="slide0019_image074.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.75 * g_height; myleft = 0.01 * g_width; myheight = 0.13 * g_height; mywidth = 0.13 * 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:"-173 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:"-173 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:"-173 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="slide0019_image075.png" 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="slide0019_image076.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.2 * g_height; myleft = 0.17 * g_width; myheight = 0.13 * 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:"-173 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:"-173 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:"-173 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 = 0.09 * g_height; mywidth = 0.11 * 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:"-173 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:"-173 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 = 0.13 * 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:"-173 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:"-173 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:"-173 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 = 0.21 * g_height; mywidth = 0.21 * 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:"-173 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:"-173 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 = 0.09 * 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:"-173 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:"-173 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 = 0.09 * g_height; mywidth = 0.07 * 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:"-173 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:"-173 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 = 0.3 * g_height; myleft = 0.78 * g_width; myheight = 0.09 * g_height; mywidth = 0.19 * 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 = 0.07 * 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 = 0.03 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><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>
</layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-173 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 = 0.31 * g_height; myleft = 0.65 * g_width; myheight = 0.02 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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-</script></div>
</layer><script> - mytop = 0.86 * g_height; myleft = 0.03 * 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 * g_height; myleft = 0 * g_width; myheight = 0.12 * 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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%;
color:#E9EB5D'>Inbred<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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%;
color:#E9EB5D'>Isogenic<br>
</span></div>
</layer><script> - mytop = 0.06 * 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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><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>
</layer><script> - mytop = 0.09 * 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:"-134 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%;
color:aqua;mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.79 * g_height; myleft = 0.83 * 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 = 0.83 * g_width; -yy = 0.79 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image078.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.84 * g_height; myleft = 0.83 * 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 = 0.83 * g_width; -yy = 0.84 * g_height; -ht = 0.02 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image079.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.79 * g_height; myleft = 0.53 * 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 = 0.53 * g_width; -yy = 0.79 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image080.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.83 * g_height; myleft = 0.53 * 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 = 0.53 * g_width; -yy = 0.83 * g_height; -ht = 0.01 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image081.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.8 * g_height; myleft = 0.23 * 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 = 0.23 * g_width; -yy = 0.8 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image082.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.18 * g_height; myleft = 0.43 * g_width; myheight = 0.09 * g_height; mywidth = 0.13 * 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 = 0.07 * g_height; mywidth = 0.12 * 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:"-341 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17'><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>
</layer></div>
</layer><script> - mytop = 0.27 * g_height; myleft = 0.32 * g_width; myheight = 0.04 * g_height; mywidth = 0.31 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.32 * g_width; -yy = 0.27 * g_height; -ht = 0.04 * g_height; -wd = 0.31 * g_width; -document.write( -'<img border=0 src="slide0019_image083.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.66 * g_height; myleft = 0.6 * g_width; myheight = 0.03 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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-</script></div>
</layer><script> - mytop = 0.64 * g_height; myleft = 0.15 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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-</script></div>
</layer><script> - mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.75 * g_width; -yy = 0.57 * g_height; -ht = 0.05 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image086.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.28 * g_height; myleft = 0.48 * g_width; myheight = 0.08 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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-</script></div>
</layer><script> - mytop = 0.62 * g_height; myleft = 0.23 * g_width; myheight = 0.16 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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-</script></div>
</layer><script> - mytop = 0.61 * g_height; myleft = 0.63 * g_width; myheight = 0.08 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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-</script></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>The next few slides
provide a short introduction to mapping the loci that are responsible for
variation in a trait such as App expression level. These modulatory regions
of the genome are sometimes called quantitative trait loci or QTLs. You may
want to do some independent reading on this topic if this is your first
exposure to QTL analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The genetic reference
population (GRP) of BXD recombinant inbred strains were originally generated
about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed
female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2
progeny. At the bottom of this slide we have schematized one chromosome pair
from three of the BXD RI strains.<span style="mso-spacerun: yes">
</span>The dashed vertical lines that lead to the final BXD RI lines involve
21 full sib matings (about 7 years of breeding). Some lines die out during
inbreeding. For example, there is no longer any BXD3 strain.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>1. Over the last decade,
our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at
Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD
strains. They have all been genotyped using about 13,700 markers (SNPs and
microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ
regions of the chromosomes as shown in the figure above.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. Chromosomes of RI GRPs
usually have about 4 times as many recombinations as those of F2 animals.
However, unlike an F2, both chromosomes of an RI are identical. Therefore,
50 RI strains contain as many recombinations as 100 F2 animals.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. BXD43 through BXD100
were generated using a special method that resulted in a further doubling of
the average recombination density per chromosome. The entire set of 80 BXDs
therefore contains as many recombinations as about 260 F2 animals.</font><br>
</td>
</tr>
</table>
</div>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
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<div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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<div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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<div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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<div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
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<div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
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lastCR;display:none'><br>
</span></div>
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</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:
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<div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt:
16'><span style='font-size:267%;color:#F6BF69'>B6 strain</span><span
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</span></div>
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<div style='mso-line-spacing:"-384 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>
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<div><script language=JavaScript><!--
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<div><script> - mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.23 * 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 = 0.13 * g_height; mywidth = 0.27 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-320 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 = 0.07 * 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 = 0.14 * 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:"-422 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:"-384 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:"-384 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:"-384 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:"-384 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="slide0020_image094.png" 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:"-350 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:"-350 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:"-350 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:"-350 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 = 0.79 * g_height; myleft = 0.05 * g_width; myheight = 0.13 * g_height; mywidth = 1.04 * 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 = 0.12 * g_height; mywidth = 1.02 * 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:"-256 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:"-256 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 = 1.02 * 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 = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 1.02 * 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'>.</span></span></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:"-233 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:"-233 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:"-233 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 = 0.17 * g_height; mywidth = 0.16 * 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:"-350 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:"-350 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 = 0.17 * 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:"-350 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:"-350 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 = 0.17 * g_height; mywidth = 0.05 * 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:"-350 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:"-350 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></div>
</layer><script> - mytop = 0.71 * g_height; myleft = 0.07 * g_width; myheight = 0.12 * g_height; mywidth = 0.16 * 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 = 0.14 * 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 = 0.05 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span
style='font-size:200%;color:#E9EB5D;display:none'><br>
</span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-233 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></div>
</layer><script> - mytop = 0.57 * g_height; myleft = -0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = -0.01 * g_width; -yy = 0.57 * g_height; -ht = 0.07 * g_height; -wd = 1.01 * g_width; -document.write( -'<img border=0 src="slide0020_image095.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.44 * g_height; myleft = 0.47 * g_width; myheight = 0.12 * 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 = 0.06 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:233%;color:#F6BF69'>Low<br>
</span></div>
</layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
17'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.58 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.13 * 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 = 0.04 * g_height; mywidth = 1.12 * 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:"-200 0 0";mso-margin-left-alt:17;
mso-text-indent-alt:17;mso-line-spacing:"-200 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>
</layer></div>
</layer><script> - mytop = 0.37 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.08 * g_width; -yy = 0.37 * g_height; -ht = 0.2 * g_height; -wd = 0.13 * g_width; -document.write( -'<img border=0 src="slide0020_image096.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.4 * g_height; myleft = 0.1 * 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 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 = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
font-size:233%;color:white'><b></b></span><span style='font-family:Palatino;
font-size:233%;color:white;display:none'><b><br>
</b></span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%;
color:white;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</layer></div>
</layer><script> - mytop = 0.4 * g_height; myleft = 0.18 * 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 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 = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
font-size:233%;color:white'><b></b></span><span style='font-family:Palatino;
font-size:233%;color:white;display:none'><b><br>
</b></span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%;
color:white;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</layer></div>
</layer><script> - mytop = 0.33 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.08 * g_width; -yy = 0.33 * g_height; -ht = 0.2 * g_height; -wd = 0.13 * g_width; -document.write( -'<img border=0 src="slide0020_image097.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></div>
</layer><script> - mytop = 0.36 * g_height; myleft = 0.18 * 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 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 = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
font-size:233%;color:white'><b></b></span><span style='font-family:Palatino;
font-size:233%;color:white;display:none'><b><br>
</b></span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%;
color:white;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</layer></div>
</layer><script> - mytop = 0.36 * g_height; myleft = 0.1 * 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 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 = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3";
font-size:233%;color:white'><b></b></span><span style='font-family:Palatino;
font-size:233%;color:white;display:none'><b><br>
</b></span></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt:
17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%;
color:white;mso-special-format:lastCR;display:none'><b><br>
</b></span></div>
</layer></div>
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</b></span></div>
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17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%;
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</b></span></div>
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-</script></div>
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<div style='mso-line-spacing:"-233 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
style='font-size:200%;color:#E9EB5D;display:none'><br>
</span></div>
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<div style='mso-line-spacing:"-233 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></div>
</layer></div>
</LAYER>
-
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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>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>This slide is
illustrates two major types of QTLs that modulate variability in
transcript-relative steady state 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 binding of a
transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms
in enhancers or may be in 3Õ UTR binding sites that affect message
stability.</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 fairly 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 overlapping
arrows in the figure.<span style="mso-spacerun: yes"> </span>The way
in which an upstream polymorphism influences a downstream difference in mRNA
abundance can be 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>
</layer>
<script language=JavaScript><!--
-//-->
-</script><script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm deleted file mode 100755 index 7a2e03db..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm +++ /dev/null @@ -1,115 +0,0 @@ -<html>
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<meta name=Description content="Jul-18-05: Discovering upstream modulatory loci">
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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:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span
style='font-family:Verdana;font-size:64%'>Discovering upstream modulatory loci</span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
</layer></div>
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<div><script language=JavaScript><!--
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</LAYER>
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<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>Please bring the Trait
Data and Analysis window to the front and look for the Interval Mapping
button. 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 Mapping Scale is
set to GENETIC</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Options: Permutation test
YES<span style="mso-spacerun: yes"> </span>(2000 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 (2000 is the default number)</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/html/webqtl_demo2.ppt_files/slide0053.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0053.htm deleted file mode 100755 index d729b467..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0053.htm +++ /dev/null @@ -1,155 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href="webqtl_demo2.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description
content="Jul-18-05: WebQTL searches for upstream controllers">
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bgcolor="#000000">
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<div><script language=JavaScript><!--
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<div><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1 * 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:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>WebQTL
searches for upstream controllers</i></span><span style='font-family:Verdana;
font-size:73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</layer></div>
</layer><script> - mytop = 0.71 * g_height; myleft = 0.34 * g_width; myheight = 0.19 * g_height; mywidth = 0.45 * 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 = 0.18 * g_height; mywidth = 0.44 * 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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style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>App maps
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style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>locus is
on Chr 7.</i></span><span style='font-size:233%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><i><br>
</i></span></span></layer></div>
</layer></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>This is a major 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 chromosomes only have a single long arm and the centromere
represents the origin of each chromosome for numerical purpose: 0
centimorgans at almost 0 megabases). The blue labels along the bottom of the
figure list a subset of the 3795 markers that were used in mapping.</font><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 chromosomes summarizes the strength of association between
variation in the phenotype (App expression differences) and the two
genotypes of all 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><font face=Verdana size=3>The red line and the red
axis to the far right provides an estimate of the effect that a QTL has on
expression of App (this estimate of the so-called additive effect tends to
be too high). 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 trait values. Multiply the
additive effect size by 2 to estimate the difference between the set of
strains that have the B/B genotype and those that have the D/D genotype at a
specific marker. For example, on distal Chr 7 the red line peaks at a value
of about 0.2. That means that this region of chromosome 2 is responsible for
a 0.4 unit expression difference between B/B strains and the D/D strains.</font><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 a
method to evaluate 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 using the 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 3 and Chr 7 under the LRS peaks. That
is somewhat reassuring. But notice that a substantial number of bootstrap
are scattered around on other chromosomes. About 30% of the bootstrap
resamples have a peak on Chr 7. That is pretty good, but does makes us
realize that the sample we are working with is still quite small and
fragile.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The horizontal dashed
lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values
associated with the suggestive and significant genome-wide probabilities
that were established by permutations of phenotypes across genotypes. We
shuffle randomly 2000 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 17.3. 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 3 is probably more than just suggestive.</font><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. 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 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 Analysis window
with the genotypes loaded into the window just like any other trait. More on
this in Section 3.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4. You can drag these
maps off of the browser window and onto your desktop. They will be saved as
PNG or PDF files. You can import them into Photoshop or other programs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>5. There is also an
option at the bottom of the page to download a 2X higher resolution image of
this plot for papers and presentations.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>6. You can also download
the results of the analysis in a text format</font><br>
</td>
</tr>
</table>
</div>
</layer>
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0054.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0054.htm deleted file mode 100755 index 64dbe68f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0054.htm +++ /dev/null @@ -1,113 +0,0 @@ -<html>
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mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>Genetic
versus Physical maps for App expression</i></span><span style='font-family:
Verdana;font-size:73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
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style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>The
difference between genetic and physical scale is analogous to measuring the </i></span></span></layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>separation
between New York and Boston in either travel hours or kilometers</i></span><span
style='font-size:150%;color:#E9EB5D'><i>.</i></span><span style='font-size:
167%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></layer></div>
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<tr>
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<td align=left colspan=1><font face=Verdana size=3>The map on the top has an
X-axis scale based on frequency of recombinations events between markers (B
to D transitions, see slide 19 for a color-coded example). These so-called
genetic maps are scaled in centimorgan (recombinations per 100 gametes). In
contrast, the physical map shown below the genetic map has an X-axis scale
based on DNA length measured in nucleotides or base-pairs. Notice the large
difference between the two maps in the size of Chr 19 (large on the genetic
scale but small on the physical scale).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Also notice the large
difference in the width of the chromosome 7 QTL peak. In mice,
recombinations occur with higher frequency toward the telomeric side (righ
sidet) of each chromosome. As a result, genetic maps are stretched out more
toward the telomere relative to a physical map. The QTL on distal Chr 7 is
therefore actually more precisely mapped than might appear looking at the
genetic map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>The physical scale is
becoming more useful than the genetic scale primarily because many other
data types can be easily superimposed on a physical map. You will see more
examples in the next several slides.</font><br>
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mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Physical
map for distal chromosome 7</span><span style='font-family:Verdana;font-size:
73%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
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no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%;
mso-text-raise:0%'><span style='font-size:167%;color:#E9EB5D'>Distal Chr 7 from
~120 and 132 Mb may modulate</span><span style='font-size:167%;color:#E9EB5D'><i>
App</i></span><span style='font-size:200%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><i><br>
</i></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>Physical map of variation
in App expression in brain on distal Chr 7 (a blow up of the whole-genome
map on the previous slide).</font><br>
</td>
</tr>
<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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Verdana size=3> You can now see that the X-axis is on a physical scale
of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. The small irregular
colored blocks and marks toward the top of the map mark the locations of
genes superimposed on the physical map. Neighboring genes are offset
slightly in the vertical axis for display purpose. Note one region of very
high gene density from about 120 to 123 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. The orange hash marks
along the X-axis represent the number of single nucleotide polymorphisms
that distinguish the two parental strains (C57BL/6J and DBA/2J) from each
other. We call this the SNP seismograph track (see Glossary for more
details). Regions with low numbers of SNP have closely matched sequences and
are less likely to contain QTLs.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4. As before, the thin
red line shows the additive effect size. By convention the positive values
signify the D alleles are associated with higher expression of App in this
region of Chr 7 than the B alleles. The maximum effect size is about +0.20
log2 expression units per D allele. The differences been the BB and DD
genotypes (BB and DD because each strain has two alleles; one per
chromosome) is therefore about 2^0.4 = 1.32; or a 32% increment in DD
relative to BB at this locus.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>5. If you scroll just
under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO
YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps
are zoomable, a feature we will exploit to evaluate candidate genes in this
QTL interval.</font><br>
</td>
</tr>
</table>
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0056.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0056.htm deleted file mode 100755 index eba3fc05..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0056.htm +++ /dev/null @@ -1,134 +0,0 @@ -<html>
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mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><span
style='font-family:Verdana;font-size:64%'>Evaluating candidate genes</span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
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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%;
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<div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>Right
position<br>
</i></span></div>
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style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>and
high </i></span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.31 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>correlation</i></span></span></layer></div>
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color:#E9EB5D'><i>= better<br>
</i></span></div>
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<div style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></span></div>
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-
<layer>
<div id=NotesObj style='display:none'>
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<td width="100%"></td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating
candidate genes (CHECKED BOXES) responsible for variability in APP
expression:</b></font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>A large number
of genes are usually in the QTL interval and are therefore POSITIONAL
CANDIDATES, but they will differ greatly in their biological and
bioinformatic plausibility. Assume that the QTL has been located between 119
and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we
might need to evaluate several hundred positional candidates. In this
particular case there are about 100 known genes in this interval. Eight of
these are highlighted in the table above with check marks in the boxes to
the left.<span style="mso-spacerun: yes"> </span>We need to highlight
and objectively score the biologically relevant subset of all 100 positional
candidate genes. We could look through gene ontologies and expression levels
to help us shorten the list. An alternate way available using WebQTL is to
generate a list of those genes in this interval that have transcripts that
co-vary in expression with App expression. That is what the table shows.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate
this table go back to the Trait Data and Analysis Form. Choose to sort
correlations by POSITION and select RETURN = 500. Then scroll down the list
to Chr 7 and review the subset of positional candidates that share
expression with App. You should see a list similar to that shown above.
Gtf3c1 is a good biological candidate and has a high covariation in
expression with App.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span
style="mso-spacerun: yes"> </span>Of course, the gene or genes
that control App expression may not be in this list. A protein coding
difference might be the ultimate cause of variation in App transcript level
and the expression covariation might be close to zero. Our list may also
simply be missing the right transcript since the microarray is not truly
comprehensive. Furthermore, even if the list contains the QT gene, an
expression difference may only have been expressed early in development or
even in another tissue such as liver. While it is important to recognize
these caveats, it is equally important to devise a rational way to rank
candidates given existing data. Coexpression is one of several criteria used
to evaluate positional candidates. We will see others in the next slide.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>3. We can also
assess the likelihood that candidates contain functional polymorphism in
promoters and enhancers that affect their expression simply by mapping the
transcripts of all candidate genes to see if they Òmap backÓ to the location
of gene itself. A transcript that maps to its own location is referred to as
a cis QTL. We essentially ask: Which of the the transcripts listed in the
Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression
that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes">
</span>The logic of this search is that if a gene controls the level of its
own expression it is also much more likely to generate other downstream
effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of
about 7.0 (D alleles are high). That is just about sufficient to declare it
to be a cis QTL. [No whole genome correction is required and a point-wise
p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly
equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
</table>
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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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mso-special-format:lastCR;display:none'><i><br>
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<tr>
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<td align=left colspan=1><font face=Verdana size=3>Even higher blow-up of
part of the Chr 7 physical map of variation in App expression in brain.<span
style="mso-spacerun: yes"> </span>The QTL region actually extends from
about 119 to 129.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
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<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br>
</td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned
in the previous slide another important approach to ranking candidates is
based on the number of sequence variants that distinguish the parental
strains. If we were sure that the sequences of the gene, its promoter, and
its enhancers were identical between the strains then we could discount--but
not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls
into this category: of 663 known SNPs in and around this gene, only four
differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially
identical-by-descent in these strains and is a less likely candidate. In
contrast, if the two alleles of the gene have dozens of functional variants
in exons, promoters, enhancers, and splice sites, then it becomes a higher
priority candidate.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face="Times New Roman" size=4>Of course it
only takes a single critical sequence variant to generate downstream
effects. The argument above is really about the prior probabilities. Where
would you place your bets given the information at hand?</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2.<span
style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL
ANALYST you will find that Ctbp2 is a particularly interesting candidate
that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2
is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain
lots of SNPs but it is also is associated with a powerful cis QTL with an
LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3.<span
style="mso-spacerun: yes"> </span>At this high magnification,
individual genes are distinct. They are color coded by their density of
SNPs. Bright orange represents those genes that have a high SNP density
(C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll
the cursor over a gene block and its name will pop up, along with
information on exon number.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>4.<span
style="mso-spacerun: yes"> </span>Beneath the physical map you will
find an INTERVAL ANALYST table that lists information on known genes in the
region on which you have zoomed the Physical Map.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>5.<span
style="mso-spacerun: yes"> </span>As always: error-checking is
important. Some genes may be missing from the Interval Analyst (recent
additions or errors of omission). In this case the Zranb1 gene that is
located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST.
Double-check the interval using the Genome Browser links (blue and beige
horizontal bars) at the top of the PHYSICAL MAP.</font><br>
</td>
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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;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Evaluating
</span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span
style='font-family:Verdana;font-size:64%'> as a candidate QTL for </span><span
style='font-family:Verdana;font-size:64%'><i>App</i></span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
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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:
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style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span
style='font-size:233%;color:#E9EB5D'><i> the </i></span></span></layer><script> - mytop = 0.06 * 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-size:233%;color:#E9EB5D'><i>Ctbp2 </i></span><span
style='font-size:233%;color:#E9EB5D'>cis QTL, </span></span></layer><script> - mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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detected </span></span></layer><script> - mytop = 0.18 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * 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:233%;color:#E9EB5D'>data set.</span><span
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</i></span></span></layer></div>
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style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span
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style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>in the INIA
data set. </span><span style='font-size:233%;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>
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<td align=left colspan=1><font face=Verdana size=3>This slide illustrates
one reason why Ctbp2 should be considered a high priority positional
candidate gene that may modulate the expression level of App.<span
style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some
brain regions (here the data are taken from the striatum).<span
style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that
modulate its own expression then these expression differencess may produce
many downstream effects. Of course, we now want to know much more about the
known biology of Ctbp2. What kind of gene is it? To begin to answer that
question we can use a number of resources listed in the LINKS page.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
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<td align=left colspan=1><font face=Verdana size=3>Notes:</font><br>
</td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Verdana size=3> The App QTL is bimodal. Perhaps there are actually two
causal factors in this region--one close to 123 Mb and the other close to
127 Mb.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. The precision of QTL
mapping depends on several factors, including the effect size and
interactions among QTLs modulating a trait, the number of genetic
individuals that are studied, and the distribution of recombinations in the
study population.<span style="mso-spacerun: yes"> </span>In the case
above, the QTL(s) are likely to be confined to the interval from 120 to 132
Mb. The bootstrap test (yellow bars shown in some of the previous slides)
can be usual for estimating the consiistency of QTL peaks.</font><br>
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mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Evaluating
</span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span
style='font-family:Verdana;font-size:64%'> using other resources</span><span
style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display:
none'><i><br>
</i></span></div>
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<td width="100%"></td>
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<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Ctbp2 should also be
considered a high priority biological candidate gene responsible for
modulating App expression levels. The<span style="mso-spacerun: yes">
</span>C-terminal binding protein 2 is a transcriptional co-repressor also
known as Ribeye.</font><font face=Times-Roman size=3> The gene produces two
transcripts encoding distinct proteins. The short form is a transcriptional
repressor that binds a Pro-X-Asp-Leu-Ser peptide motif common to adenoviral
oncoprotein E1a and a related motif in BKLF. This short form also interacts<span
style="mso-spacerun: yes"> </span>with several transcription factors
including EVI1, ZFPM1, and<span style="mso-spacerun: yes">
</span>ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component
of specialized synapses in photoreceptors. Both proteins contain a NAD+
binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
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<td align=left colspan=1><font face=Verdana size=3>Notes:</font><br>
</td>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>1. To find out more about
CTBP2 protein and the Ctbp2 gene, link to iHOP at
http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>Try Arrowsmith at
http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>2. Both APP and CTBP2 are
involved in oxidoreducatase activity or Notch signalling. To estabilish this
common gene ontology visit NCBI<span style="mso-spacerun: yes">
</span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span
style="mso-spacerun: yes"> </span>and enter each gene symbol.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>3. You can get intersting
hints regarding Ctbp2 expression partners by examining the genetic
correlations between Ctbp2 probe set 1422887_a_at and all other transcripts
on the M430 Affymetrix array. Use the Striatum data set because we already
know from previous work (the previous slide) that this gene is a cis
QTL.<span style="mso-spacerun: yes"> </span>You should be able to show
that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The
negative genetic correlation with E2f4 is even stronger. The transcript also
has a high positive genetic correlation with Rdh14. Of particualr interest
with respect to APP protein processing, Ctbp2 covaries positiviely with
Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</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><br>
</td>
</tr>
</table>
</div>
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<script language=JavaScript><!--
-//-->
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm deleted file mode 100755 index 2f1c5b7b..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm +++ /dev/null @@ -1,139 +0,0 @@ -<html>
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<div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans";
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292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
292;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'>Summary of Part 2:</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
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<layer>
<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%'></div>
</layer>
<script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.96%;font-family:Arial'>1.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Covered the basics of QTL
analysis and mapping.<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.92 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.71%;font-family:Arial'>2.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Reviewed difference between
genetic and physical maps.<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.95 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.62%;font-family:Arial'>3.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Discussed interpreting features
of QTL maps including the </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * 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:200%;
color:#E9EB5D;mso-color-index:3'>LRS function, the additive effect function,
the bootstrap bars, </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * 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:200%;
color:#E9EB5D;mso-color-index:3'>and the permutation thresholds.<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
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color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.51%;font-family:Arial'>4.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Illustrated technics to
generate a list of positional candidates.<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.65%;font-family:Arial'>5.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>Discussed some factors used to
evaluate candidate genes.</span></span></layer></div>
</layer></div>
</layer><script> - mytop = 0.58 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.06 * 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 = 0.05 * g_height; mywidth = 1.06 * 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:200%;
color:#E9EB5D;mso-color-index:3'>What does a QTL signify? A good QTL is a claim
that a particular </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * 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-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'>chromosomal region contains a causal source of
variation in the </span></span></layer><script> - mytop = 0.1 * 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-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'>phenotype. The importance of this hypothesis
depends on the </span></span></layer><script> - mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.92 * 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:200%;
color:#E9EB5D;mso-color-index:3'>quality and relevance of the phenotype and the
statistical </span></span></layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * 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-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'>strength of the QTL. As usual, test and be
skeptical.</span></span></layer></div>
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0061.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0061.htm deleted file mode 100755 index a2816092..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0061.htm +++ /dev/null @@ -1,112 +0,0 @@ -<html>
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<div><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233;
mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'>Test
Questions</span><span style='font-family:Verdana;font-size:73%;mso-special-format:
lastCR;display:none'><i><br>
</i></span></div>
</layer></div>
</layer><script> - mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 1.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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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%'><span style='font-size:233%;color:#E9EB5D'>1. Evaluate
candidates for the Chr 3 </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span
style='font-size:233%;color:#E9EB5D'> QTL.</span><span style='font-size:233%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</layer><script> - mytop = 0.24 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1 * 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 = 1 * 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'>2. Do </span><span
style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:
233%;color:#E9EB5D'> and </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span
style='font-size:233%;color:#E9EB5D'> expression share any </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-size:233%;color:#E9EB5D'>other QTLs
beside that on Chr 7?</span><span style='font-size:233%;color:#E9EB5D;
mso-special-format:lastCR;display:none'><i><br>
</i></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:
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style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>3. Can you
exploit literature mining tools to </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.05 * 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'>find strong
relation between </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span
style='font-size:233%;color:#E9EB5D'> and </span><span style='font-size:233%;
color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'>? </span><span
style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></layer></div>
</layer><script> - mytop = 0.66 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1.1 * 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 = 1.1 * 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'>4. Why might
the cis QTL for </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span
style='font-size:233%;color:#E9EB5D'> expression </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * 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'>only be
detected in the striatum data set?</span><span style='font-size:233%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></span></layer></div>
</layer></div>
</LAYER>
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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/html/webqtl_demo2.ppt_files/slide0062.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0062.htm deleted file mode 100755 index 6b671799..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0062.htm +++ /dev/null @@ -1,109 +0,0 @@ -<html>
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<div style='text-align:left;font-family:"Gill Sans";font-weight:normal;
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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>
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</layer><script> - mytop = 0.16 * g_height; myleft = 0.06 * g_width; myheight = 0.24 * g_height; mywidth = 0.9 * 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 = 0.24 * g_height; mywidth = 0.87 * 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:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * 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:82%'>rwilliam@nb.utmem.edu<br>
</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
style='text-align:left'><span style='font-size:82%'><br>
</span></span></layer><script> - mytop = 0.16 * 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
style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR;
display:none'><br>
</span></span></layer></div>
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</layer><script> - mytop = 0.27 * g_height; myleft = 0.09 * g_width; myheight = 0.07 * g_height; mywidth = 0.5 * 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%'><span style='font-family:"Gill Sans";font-size:300%;
color:#E9EB5D'>kmanly@utmem.edu</span></div>
</layer><script> - mytop = 0.83 * g_height; myleft = 0.04 * g_width; myheight = 0.1 * g_height; mywidth = 1.01 * 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 = 0.98 * 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:200%;
color:#E9EB5D'>The </span><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D'><i>App</i></span><span style='font-family:"Gill Sans";
font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part
of an </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * 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:200%;
color:#E9EB5D'>ongoing study of R. Wiliams and R. Homayouni (July 15, 2005)</span><span
style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D;mso-special-format:
lastCR;display:none'><br>
</span></span></layer></div>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Verdana size=3>END</font><br>
</td>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
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</head>
<body bgcolor=black text=white link=white vlink=white alink=white
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<td width=100% id="p1" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('1')" id=AREF>GeneNetwork and WebQTL:</a></b></font></td>
</tr>
</table>
<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>Slide 2</a></b></font></td>
</tr>
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<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>Slide 3</a></b></font></td>
</tr>
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<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><font face="Gill Sans">Search
results</font></a></b></font></td>
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href="javascript:parent.base.Slide('5')" id=AREF>"First page of data:"</a></b></font></td>
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<td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td>
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for App on..."</a></b></font></td>
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data the..."</a></b></font></td>
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href="javascript:parent.base.Slide('9')" id=AREF>"App expression after
windsorizing"</a></b></font></td>
</tr>
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<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>"Discovering shared
expression patterns"</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>"Transcript
neighborhoods"</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>"App and Atcay
transcript scatterplot"</a></b></font></td>
</tr>
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<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
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eight of..."</a></b></font></td>
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<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>App transcript coexpression
neighborhood</a></b></font></td>
</tr>
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<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>"Correlations of App
with classical..."</a></b></font></td>
</tr>
</table>
<table width=100%>
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<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
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with..."</a></b></font></td>
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<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
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<td width=100% id="p18" ><font face=Arial size=2><b><a
href="javascript:parent.base.Slide('18')" id=AREF>Contact for comments and
improvements:</a></b></font></td>
</tr>
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</body>
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<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
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href="webqtl_demo2_part1.ppt.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>GeneNetwork and WebQTL:</a></b></font></td>
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<td colspan=1><font face=Arial size=2>Part 1: How to study expression
variation and covariation (slides 2–16)</font></td>
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<tr>
<td colspan=1></td>
<td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators
(slides 17–30)</font></td>
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<br>
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<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>Slide 2</a></b></font></td>
</tr>
</table>
<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>Slide 3</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><font face="Gill Sans">Search
results</font></a></b></font></td>
</tr>
</table>
<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>"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 Trait Data and
Analysis Form</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>"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: Metadata for each
resource</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>"Expression estimates
for App on..."</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>Expression estimates for App on the
Trait Data form</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>"Critiquing the App
data the..."</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>Critiquing the App data the Trait Data</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>"App expression after
windsorizing"</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>App expression after windsorizing</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>"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= 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>"Transcript
neighborhoods"</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>Transcript neighborhoods</font></td>
</tr>
</table>
<br>
<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>"App and Atcay
transcript scatterplot"</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>App and Atcay transcript scatterplot</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>"App transcript and
eight of..."</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>App transcript and eight of its
neighbors</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>App transcript coexpression
neighborhood</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>"Correlations of App
with classical..."</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>Correlations of App with classical
traits</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>"Network Graph of App
with..."</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>Network Graph of App with classical
traits</font></td>
</tr>
</table>
<br>
<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>"Summary of Part 1:"</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>Summary of Part 1:</font></td>
</tr>
</table>
<br>
<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>Contact for comments and
improvements:</a></b></font></td>
</tr>
</table>
</body>
</html>
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- else if( (event.which == 32) || (event.which == 13) || HitOK( event ) ) { - if( window.name == "PPTSld" ) - parent.PPTSld.DocumentOnClick(); - else - parent.M_GoNextSld(); - } - else if ( parent.IsFullScrMode() && ((event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12)) ) - parent.M_GoNextSld(); - else if ( parent.IsFullScrMode() && ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8)) ) - parent.M_GoPrevSld(); - - return; - } - - if( IsNts() ) return; - - if(parent.IsFullScrMode() && event.keyCode == 27 && !parent.HideMenu() ) - parent.base.CloseFullScreen(); - else if( (event.keyCode == 32) || (event.keyCode == 13) ) - { - if( window.name == "PPTSld" ) - parent.PPTSld.DocumentOnClick(); - else - parent.M_GoNextSld(); - } - else if ( parent.IsFullScrMode() && ((event.keyCode == 78) || (event.keyCode == 110)) ) - parent.M_GoNextSld(); - else if ( parent.IsFullScrMode() && ((event.keyCode == 80) || (event.keyCode == 112)) ) - parent.M_GoPrevSld(); -} - -function DocumentOnClick(event) -{ - if ( g_doAdvOnClick && !parent.IsFullScrMode() ) { - parent.base.TP_GoToNextSld(); - return; - } - - if ( parent.base.msie < 0 ) - { - if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || - (event && ( (event.which == 32) || (event.which == 13) ) ) ) - parent.M_GoNextSld(); - return; - } - if( IsNts() || (parent.IsFullScrMode() && parent.HideMenu() ) ) return; - if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || - (event && ( (event.keyCode==32) || (event.keyCode == 13) ) ) ) - parent.M_GoNextSld(); -} -
- -var g_supportsPPTHTML = SupportsPPTHTML(), g_scaleInFrame = true, gId="", g_bgSound="", - g_scaleHyperlinks = false, g_allowAdvOnClick = true, g_showInBrowser = false, g_doAdvOnClick = false; - - var g_showAnimation = 0; -var g_hasTrans = false, g_autoTrans = false, g_transSecs = 0; -var g_animManager = null; - -var ENDSHOW_MESG="End of slide show, click to exit.", SCREEN_MODE="Frames", gIsEndShow=0, NUM_VIS_SLDS=18, SCRIPT_HREF="script.js", FULLSCR_HREF="fullscreen.htm"; -var gCurSld = gPrevSld = 1, g_offset = 0, gNtsOpen = gHasNts = gOtlTxtExp = gNarrationPaused = false, gOtlOpen = true -window.gPPTHTML=SupportsPPTHTML() -var g_hideNav = 0; -function UpdNtsPane(){ PPTNts.location.replace( MHTMLPrefix+GetHrefObj( gCurSld ).mNtsHref ) } -function UpdNavPane( sldIndex ){ if(gNavLoaded) PPTNav.UpdNav() } -function UpdOtNavPane(){ if(gOtlNavLoaded) PPTOtlNav.UpdOtlNav() } -function UpdOtlPane(){ if(gOtlLoaded) PPTOtl.UpdOtl() } -function SetHasNts( fVal ) -{ - if( gHasNts != fVal ) { - gHasNts=fVal - UpdNavPane() - } -} - -function ToggleVNarration() -{ - if ( base.msie < 0 ) { - PPTSld.ToggleSound( false, PPTSld.document.NSPlay ); - return; - } - - rObj=PPTSld.document.all("NSPlay") - if( rObj ) { - if( gNarrationPaused ) - rObj.Play() - else - rObj.Pause() - - gNarrationPaused=!gNarrationPaused - } -} - -function PrevSldViewed(){ GoToSld( GetHrefObj(gPrevSld).mSldHref ) } -function HasPrevSld() { return ( gIsEndShow || ( g_currentSlide != 1 && GetHrefObj( g_currentSlide-1 ).mVis == 1 )||( GetCurrentSlideNum() > 1 ) ) } -function HasNextSld() { return (GetCurrentSlideNum() != GetNumSlides()) } -function StartEndShow() -{ -// g_hideNav = 1; -// PPTNav.location.reload(); - if( PPTSld.event ) PPTSld.event.cancelBubble=true - - doc=PPTSld.document - doc.open() - doc.writeln('<html><head><script > /*defer>*/ g_ctxmenu = 0; ' + - 'if( parent.base.msie < 0 ) { document.captureEvents(Event.KEYPRESS); document.captureEvents(Event.MOUSEDOWN); document.onkeypress = _KPH; document.onmousedown = _KPH; } ' + - 'function DocumentOnClick(event) { return _KPH(event); } function IsContextMenu() { return (g_ctxmenu ==1); } ' + - 'function _KPH(event)' + - '{ ' + - 'if ( parent.base.msie < 0 && (parent.IsFullScrMode() ) && event ) { if ( (!parent.IsMac() && event.which == 3) || ( parent.IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { return parent.KPH(event); } ' + - ' else if (event.which == 27 || event.which == 32 || event.which == 13 || parent.HitOK( event ) || (event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12) ) { if ( IsContextMenu() ) { return parent.KPH(event); } parent.base.CloseFullScreen(); return; } ' + - ' else if ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8) ) { parent.M_GoPrevSld(); } } ' + - 'if( parent.HideMenu() ) return; if( (parent.IsFullScrMode() ) && event) { if ( (event.keyCode==27 || event.keyCode == 13 || event.keyCode==32 || event.type=="click" ) || (event.keyCode == 78) || (event.keyCode == 110) ) { parent.base.CloseFullScreen(); }' + - ' else if ( (event.keyCode == 80) || (event.keyCode == 112) ) { parent.M_GoPrevSld(); } } } function Unload() { parent.gIsEndShow=0; } function SetupEndShow() { if ( !parent.IsFullScrMode() ) { return; } else { parent.PPTNav.location.reload(); } parent.gIsEndShow=1; if ( parent.g_docTable[0].type != "jpeg" ) { if ( parent.base.msie < 0 ) {parent.createCM(); } document.oncontextmenu=parent._CM; } }</script></head><body scroll=\"no\" onclick=\"DocumentOnClick(event)\" onkeypress=\"_KPH(event)\" bgcolor=\"black\" onload=\"SetupEndShow()\" onunload=\"Unload()\"><center><p><font face=Tahoma color=white size=2><br><b>' + ENDSHOW_MESG + '</b></font></p></center></body></html>') - doc.close() -} -function SetSldVisited(){ gDocTable[gCurSld-1].mVisited=true } -function IsSldVisited(){ return gDocTable[gCurSld-1].mVisited } -function hrefList( sldHref, visible, sldIdx ) -{ - this.mSldHref= this.mNtsHref = sldHref - this.mSldIdx = sldIdx - this.mOrigVis= this.mVis = visible - this.mVisited= false -} -var gDocTable = new Array(
- new hrefList("slide0001.htm", 1, 1),
- new hrefList("slide0002.htm", 1, 2),
- new hrefList("slide0003.htm", 1, 3),
- new hrefList("slide0004.htm", 1, 4),
- new hrefList("slide0005.htm", 1, 5),
- new hrefList("slide0006.htm", 1, 6),
- new hrefList("slide0007.htm", 1, 7),
- new hrefList("slide0008.htm", 1, 8),
- new hrefList("slide0009.htm", 1, 9),
- new hrefList("slide0010.htm", 1, 10),
- new hrefList("slide0011.htm", 1, 11),
- new hrefList("slide0012.htm", 1, 12),
- new hrefList("slide0013.htm", 1, 13),
- new hrefList("slide0014.htm", 1, 14),
- new hrefList("slide0015.htm", 1, 15),
- new hrefList("slide0016.htm", 1, 16),
- new hrefList("slide0017.htm", 1, 17),
- new hrefList("slide0018.htm", 1, 18)
-);
- -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( 16,0,1);
-makeSlide( 17,1,1);
- -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 = 18, - 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("/") ) + "/" + "webqtl_demo2_part1.ppt_files"; -var g_showoutline = 1; -var g_shownotes = includeNotes; -var g_currentSlide = INITSLIDENUM, g_prevSlide = INITSLIDENUM; 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- else - g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "ie" ); - if ( !g_hiddenSlide[i] ) count_hidden++; - else UpdateLastVisibleSlide( i+1 ); - } -} - -function navArray( numSlides ) { -count_hidden = 0; - g_docTable = new Array(); - for( i=0; i<numSlides; i++ ) { - j = numSlides + i + 1; - var str = slidenum( j ) +".htm"; - if( g_notesTable[i] == 1 ) - g_docTable[i] = new hrefList( str, slidenum(i+1 ) + "_notes_pane.htm", g_hiddenSlide[i], i+1-count_hidden, "nav" ); - else - g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "nav" ); - if ( !g_hiddenSlide[i] ) count_hidden++; - else UpdateLastVisibleSlide( i+1 ); - } -} - -function LoadHTMLVersion() { - var os = window.navigator.platform.indexOf("Mac"); - if ( (msie || isnav ) && ( (os < 0 && ver >= 4 ) || ( os >= 0 && ver >= 5 ) || (os >=0 && msie < 0 && ver >= 4 ) ) ){ - if ( msie >= 0 ) { - if ( isIEFiles > 0 ) - ieArray( 18 ); - else if ( isFLATFiles > 0 ){ - /*if ( IsFramesMode() ) - StatusPlay("This presentation is optimized for use with older versions of your browser. Since you are using a more recent version of Microsoft Internet Explorer or Netscape Navigator, consider optimizing this presentation to take advantage of your current version's advanced capabilities."); */ - jpegArray( 18 ); - } - else - window.location.replace( "webqtl_demo2_part1.ppt_files/error.htm" ); - } - else { - if ( isNAVFiles > 0 && ver < 5) - navArray( 18 ); - else if ( isFLATFiles > 0 ) { - /* if ( IsFramesMode() ) - StatusPlay("This presentation is optimized for use with older versions of your browser. Since you are using a more recent version of Microsoft Internet Explorer or Netscape Navigator, consider optimizing this presentation to take advantage of your current version's advanced capabilities."); */ - jpegArray( 18 ); - } - else - window.location.replace( "webqtl_demo2_part1.ppt_files/error.htm" ); - } -} -else { - /* - if ( IsFramesMode() && !isWebTV() ) - StatusPlay("This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator."); - */ - if ( isFLATFiles <= 0 ) { - /* if ( IsFramesMode() ) - window.alert("This presentation contains content that your browser may not be able to display properly. This presentation is optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); - */ - window.location.replace( "webqtl_demo2_part1.ppt_files/error.htm" ); - } - /* - else if ( IsFramesMode() && !isWebTV() ) - StatusPlay( "This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); - */ - jpegArray ( 18 ); - } - -} - -function isWebTV() { - if ( window.navigator.appName.indexOf( 'WebTV' ) >= 0 ) - return true; - return false; -} - -var count; -var statusText; -var statusfirst = 0; - function display50( text ) -{ - len = text.length; - if ( len < 50 && count < 2) { - window.status = text; - window.setTimeout( "repeat()", 300 ); - } - else { - var period = 200; - window.status = text; - newtext = text.substring( 1, len ); - if ( statusfirst ) { - statusfirst = 0; - period = 2000; - } - window.setTimeout( "display50( newtext )", period ); - } -} -function repeat( ) { - count++; - statusfirst = 1; - display50( statusText ); -} - -function StatusPlay( text ) { - count = 0; - statusText = text; - repeat( ); - } -function makeSlide( i, notes, visible ) { - g_notesTable[i] = notes; - g_hiddenSlide[i] = visible; -} - diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.htm deleted file mode 100755 index d17c2490..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content="Aug-15-05: GeneNetwork and WebQTL:">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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{left:0px !important;
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--
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-</script><script for=window event=onload language=JavaScript><!--
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:.88%;left:3.31%;width:84.37%;height:9.89%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232;
mso-text-indent-alt:0;position:absolute;top:0%;left:1.25%;width:97.95%;
height:100.0%'><span style='font-size:105%'><i>GeneNetwork and WebQTL:</i></span><span
style='font-size:68%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
</div>
<div style='position:absolute;top:24.02%;left:5.82%;width:69.0%;height:50.7%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='position:absolute;top:0%;left:2.87%;width:97.12%;
height:71.08%'>
<div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:0%;left:0%;width:92.68%;height:53.43%'><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'>Part
1: How to study </span></span><span style='position:absolute;top:31.19%;
left:8.1%;width:91.89%'><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>expression variation and </span></span><span style='position:absolute;
top:61.46%;left:8.1%;width:91.89%'><span style='font-size:106%;color:#E9EB5D;
mso-color-index:3'>covariation (slides 2–16)<br>
</span></span></div>
<div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt:
56;position:absolute;top:63.23%;left:0%;width:100.0%;height:36.76%'><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'>Part
2. Discovering upstream </span></span><span style='position:absolute;
top:45.33%;left:7.5%;width:89.32%'><span style='font-size:106%;color:#E9EB5D;
mso-color-index:3'>modulators (slides 17–30)</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></span></div>
</div>
</div>
<img border=0 src="slide0001_image001.png" 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:"-346 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:"-346 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:66.43%;left:3.44%;width:80.66%;
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'><i>PowerPoint ÒNormal viewÓ has notes that may be </i></span></span><span
style='position:absolute;top:50.76%;left:0%;width:86.53%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'><i>useful companions to these slides.</i></span><span style='font-family:
"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:3;mso-special-format:
lastCR;display:none'><br>
</span></span></div>
<div class=O style='position:absolute;top:10.95%;left:6.35%;width:55.23%;
height:7.42%'><span style='font-family:"Gill Sans";font-size:283%;color:#E9EB5D'><i>a
PowerPoint Presentation</i></span><span style='font-family:"Gill Sans";
font-size:317%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
<div class=O style='position:absolute;top:92.4%;left:75.23%;width:26.49%;
height:3.88%'><span style='font-family:Helvetica;font-size:167%;color:#E9EB5D'><i>RWW
07.23.2005</i></span></div>
<div class=O style='position:absolute;top:81.97%;left:3.44%;width:77.21%;
height:11.48%'>
<div style='position:absolute;top:0%;left:0%;width:88.16%;height:49.23%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'><i>You can also download this PowerPoint at<br>
</i></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>ftp://atlas.utmem.edu/public/webqtl_demo2.ppt </i></span><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3;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>Welcome to a short
demonstration of the GeneNetwork and its WebQTL module. Please adjust the
size of the windows on your monitor so that you can see part of this page, as
well as GeneNetwork windows. WebQTL produces a large number of new windows,
so you may need to modify your browser preferences to permit pop-ups. In this
demonstration, we explore one important transcript expressed in the brain:
the amyloid beta precursor protein messenger RNA. A protein product of this
mRNA, the APP protein, is associated with AlzheimerÕs 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>My thanks to Dr. Robert
F. Clark and Wenli Cai for testing this PowerPoint demonstration and making
many improvements.</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. Edits July 13, 2005 by RW and RFC. Edit July 14, 2005
by WC. Final edits by RF Clark, July 22, 2005.</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/html/webqtl_demo2_part1.ppt_files/slide0001_image001.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_image001.png Binary files differdeleted file mode 100755 index a1cb20e4..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_image001.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_notes_pane.htm deleted file mode 100755 index 7c670210..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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
demonstration of the GeneNetwork and its WebQTL module. Please adjust the
size of the windows on your monitor so that you can see part of this page, as
well as GeneNetwork windows. WebQTL produces a large number of new windows,
so you may need to modify your browser preferences to permit pop-ups. In this
demonstration, we explore one important transcript expressed in the brain:
the amyloid beta precursor protein messenger RNA. A protein product of this
mRNA, the APP protein, is associated with AlzheimerÕs 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>My thanks to Dr. Robert
F. Clark and Wenli Cai for testing this PowerPoint demonstration and making
many improvements.</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. Edits July 13, 2005 by RW and RFC. Edit July 14, 2005
by WC. Final edits by RF Clark, July 22, 2005.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002.htm deleted file mode 100755 index 8627e129..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<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="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; -//-->
-</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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img
border=0 src="slide0002_image002.png" style='position:absolute;top:8.3%;
left:.39%;width:86.35%;height:86.21%'><img border=0 src="slide0002_image003.png"
style='position:absolute;top:34.27%;left:59.07%;width:12.18%;height:14.48%'>
<div style='position:absolute;top:46.64%;left:85.43%;width:16.29%;height:12.01%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:2.94%;left:5.69%;width:93.49%;
height:91.17%'>
<div style='mso-line-spacing:"-224 0 0";position:absolute;top:0%;left:0%;
width:91.3%;height:51.61%'><span style='font-family:"Gill Sans";font-size:217%;
color:#E9EB5D;mso-color-index:3'>Choose<br>
</span></div>
<div style='mso-line-spacing:"-224 0 0";position:absolute;top:48.38%;
left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans";
font-size:217%;color:#E9EB5D;mso-color-index:3'>database</span></div>
</div>
</div>
<div style='position:absolute;top:62.19%;left:86.62%;width:21.05%;height:12.72%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:6.94%;left:5.03%;width:89.93%;
height:86.11%'>
<div style='position:absolute;top:0%;left:0%;width:100.0%;height:51.61%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>Enter<br>
</span></div>
<div style='mso-line-spacing:"-224 0 0";position:absolute;top:48.38%;
left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans";
font-size:217%;color:#E9EB5D;mso-color-index:3'><i>APP</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>
<div style='position:absolute;top:77.73%;left:85.96%;width:12.58%;height:12.72%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:6.94%;left:8.42%;width:91.57%;
height:86.11%'>
<div style='position:absolute;top:0%;left:0%;width:91.95%;height:51.61%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>Select<br>
</span></div>
<div style='mso-line-spacing:"-224 0 0";position:absolute;top:48.38%;
left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans";
font-size:217%;color:#E9EB5D;mso-color-index:3'>search</span></div>
</div>
</div>
<div style='position:absolute;top:.88%;left:0%;width:111.92%;height:9.18%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div style='position:absolute;top:0%;left:.94%;width:99.05%;height:80.76%'>
<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:"-220 0 -216";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'>PART 1: How to study variation and
covariation</span></div>
</div>
</div>
<div style='position:absolute;top:15.54%;left:85.82%;width:16.15%;height:22.43%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='mso-line-spacing:"-224 0 0";position:absolute;top:1.57%;
left:6.55%;width:94.26%;height:94.48%'><span style='position:absolute;
top:0%;left:0%;width:91.3%'><span style='font-family:"Gill Sans";font-size:
217%;color:#E9EB5D;mso-color-index:3'>Choose<span style="mso-spacerun:
yes"> </span></span></span><span style='position:absolute;top:25.0%;
left:0%;width:91.3%'><span style='font-family:"Gill Sans";font-size:217%;
color:#E9EB5D;mso-color-index:3'>species, </span></span><span style='position:
absolute;top:49.16%;left:0%;width:91.3%'><span style='font-family:"Gill Sans";
font-size:217%;color:#E9EB5D;mso-color-index:3'>group, </span></span><span
style='position:absolute;top:73.33%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>and type</span></span></div>
</div>
<img border=0 src="slide0002_image004.png" style='position:absolute;top:71.37%;
left:48.87%;width:12.58%;height:13.78%'></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>Please link to the web
site:<span style="mso-spacerun: yes"> </span>http://www.genenetwork.org</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>To begin a search you
make choices about what species, group, and database to explore.</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>For this demonstration
enter APP as above and click on the SEARCH button. Make sure that the DEFAULT
SETTINGS are species = Mouse, Group = BXD, Type = Whole Brain, and Database =
INIA BRAIN mRNA M430 (Apr05) PDNN.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>1. The GeneNetwork and
WebQTL are often used to work with public data sets. However, it is possible
to enter and analyze your own data for specific genetic reference populations
such as the BXD genetic reference population of mice or the HXB strains of rat.
Entering your own data is a more advanced topic, but if you click on the HOME
pop-down menu (upper left), you will see ÒEnter Trait DataÓ that will explain
the process.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>2.</font><font
face=Helvetica size=3> For help on advanced searching methods read the left
side of the page (INTRODUCTION).<span style="mso-spacerun: yes">
</span>If you make a search term too complex, you may get no hits (try
entering Òamyloid betaÓ for example). If you make it too simple, you may also
get too many.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>3.</font><font
face=Helvetica size=3> Use the asterisk * as a wildcard. For example, to find
all <i>Hoxb</i> transcripts, search for Hoxb*.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>4.</font><font
face=Helvetica size=3> In some cases you can also research for transcripts
and genes using special search strings such as Ò</font><font face=Geneva
size=3>Mb = (Chr1, 100 102)Ó to find all genes on Chromosome 1 between 98 and
104 megabases (donÕt actually use the quotes). Details are described at </font><font
face=Verdana size=3>http://www.genenetwork.org/searchHelp.html</font><font
face=Geneva size=3>.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>5.<span
style="mso-spacerun: yes"> </span>These INFO buttons provide
links to data about the different data types. Try them.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>6.<span
style="mso-spacerun: yes"> </span>The SET TO DEFAULT button is used to
change the database default setting to match your typical search categories.</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/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png Binary files differdeleted file mode 100755 index 2eb797be..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png Binary files differdeleted file mode 100755 index d1370484..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png Binary files differdeleted file mode 100755 index a4f088b8..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm deleted file mode 100755 index 5f7740c5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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>Please link to the web
site:<span style="mso-spacerun: yes"> </span>http://www.genenetwork.org</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>To begin a search you
make choices about what species, group, and database to explore.</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>For this demonstration
enter APP as above and click on the SEARCH button. Make sure that the DEFAULT
SETTINGS are species = Mouse, Group = BXD, Type = Whole Brain, and Database =
INIA BRAIN mRNA M430 (Apr05) PDNN.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>1. The GeneNetwork and
WebQTL are often used to work with public data sets. However, it is possible
to enter and analyze your own data for specific genetic reference populations
such as the BXD genetic reference population of mice or the HXB strains of rat.
Entering your own data is a more advanced topic, but if you click on the HOME
pop-down menu (upper left), you will see ÒEnter Trait DataÓ that will explain
the process.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>2.</font><font
face=Helvetica size=2> For help on advanced searching methods read the left
side of the page (INTRODUCTION).<span style="mso-spacerun: yes">
</span>If you make a search term too complex, you may get no hits (try
entering Òamyloid betaÓ for example). If you make it too simple, you may also
get too many.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>3.</font><font
face=Helvetica size=2> Use the asterisk * as a wildcard. For example, to find
all <i>Hoxb</i> transcripts, search for Hoxb*.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>4.</font><font
face=Helvetica size=2> In some cases you can also research for transcripts
and genes using special search strings such as Ò</font><font face=Geneva
color="#222222" size=2>Mb = (Chr1, 100 102)Ó to find all genes on Chromosome
1 between 98 and 104 megabases (donÕt actually use the quotes). Details are
described at </font><font face=Verdana color=black size=2>http://www.genenetwork.org/searchHelp.html</font><font
face=Geneva color="#222222" size=2>.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>5.<span
style="mso-spacerun: yes"> </span>These INFO buttons provide
links to data about the different data types. Try them.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>6.<span
style="mso-spacerun: yes"> </span>The SET TO DEFAULT button is used to
change the database default setting to match your typical search categories.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003.htm deleted file mode 100755 index 5507bd68..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img
border=0 src="slide0003_image005.png" style='position:absolute;top:34.27%;
left:59.07%;width:12.18%;height:14.48%'>
<div style='position:absolute;top:.88%;left:.79%;width:105.69%;height:9.18%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div style='position:absolute;top:0%;left:1.0%;width:98.99%;height:80.76%'>
<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:"-220 0 -216";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'>Please also use the Glossary, FAQ, and
News</span></div>
</div>
</div>
<img border=0 src="slide0003_image006.png" style='position:absolute;top:10.07%;
left:1.72%;width:69.66%;height:60.95%'><img border=0
src="slide0003_image008.png" style='position:absolute;top:9.18%;left:18.8%;
width:12.58%;height:13.78%'><img border=0 src="slide0003_image009.png"
style='position:absolute;top:49.11%;left:38.27%;width:60.0%;height:48.58%'></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>SHORT DETOUR to the HELP
menu. If you are new to the GeneNetwork, you may find it helpful to review
the The Glossary and FAQ pages shown above. We are in the process of making
ÒliveÓ demos for some of the key modules in the GeneNetwork. Check the NEWS
every month or two to find out about new features.</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>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png Binary files differdeleted file mode 100755 index d1370484..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image006.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image006.png Binary files differdeleted file mode 100755 index c9843a48..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image006.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image008.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image008.png Binary files differdeleted file mode 100755 index 504177df..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image008.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image009.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image009.png Binary files differdeleted file mode 100755 index 901c77a0..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image009.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm deleted file mode 100755 index b8742fdc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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>SHORT DETOUR to the HELP
menu. If you are new to the GeneNetwork, you may find it helpful to review
the The Glossary and FAQ pages shown above. We are in the process of making
ÒliveÓ demos for some of the key modules in the GeneNetwork. Check the NEWS
every month or two to find out about new features.</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/html/webqtl_demo2_part1.ppt_files/slide0004.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004.htm deleted file mode 100755 index ab2d96f6..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content="Aug-15-05: Search results">
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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{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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img
border=0 src="slide0004_image010.png" style='position:absolute;top:9.18%;
left:3.31%;width:68.74%;height:90.81%'><img border=0
src="slide0004_image012.png" style='position:absolute;top:63.78%;left:63.57%;
width:14.7%;height:6.53%'>
<div class=O style='position:absolute;top:45.93%;left:80.13%;width:18.94%;
height:47.17%'>
<div style='mso-line-spacing:"-224 0 0";position:absolute;top:0%;left:0%;
width:100.0%;height:44.94%'><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'>Highlight </span></span><span style='position:absolute;
top:24.16%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";
font-size:217%;color:#E9EB5D;mso-color-index:3'>this probe </span></span><span
style='position:absolute;top:49.16%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>set in red </span></span><span style='position:absolute;top:73.33%;
left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;
color:#E9EB5D;mso-color-index:3'>and</span><span style='font-family:"Gill Sans";
font-size:217%;color:#E9EB5D;mso-color-index:3;display:none'><i><br>
</i></span></span></div>
<div style='mso-line-spacing:"-224 0 0";position:absolute;top:43.82%;
left:0%;width:100.0%;height:56.17%'><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'>click. You </span></span><span
style='position:absolute;top:20.0%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>do NOT </span></span><span style='position:absolute;top:39.33%;left:0%;
width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
mso-color-index:3'>have to </span></span><span style='position:absolute;
top:59.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";
font-size:217%;color:#E9EB5D;mso-color-index:3'>select the </span></span><span
style='position:absolute;top:78.66%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3'>checkbox</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 style='position:absolute;top:-4.41%;left:1.72%;width:84.63%;height:18.19%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='position:absolute;top:29.12%;left:1.4%;width:97.18%;
height:42.71%'><span style='font-size:82%'>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>RESULTS OF THE APP
SEARCH.<span style="mso-spacerun: yes"> </span>A search of the INIA
Brain database generates 18 matches, 10 of which are shown above. The
GeneNetwork will display several hundred matches in pages of 40 each. If a
search generates a larger numbers of hits, then you will need to refine
search terms.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>1. APP is a great
transcript to introduce you to the complexity and power of new array
platforms that often provide ÒalternativeÓ expression estimates for single
genes. There are seven probe sets that target different parts of the APP
transcript. Which of the alternative measurements is most appropriate and
informative? Have a look at the FAQ page for more on this topic, but general
advice: 1. be skeptical and try to validate that the correct transcript and
gene is being measured; 2. check what part of the transcript is complementary
to the probes; 3. evaluate the performance of individual probes based on
expression level, signal-to-noise and other error terms such as the standard
deviation and error.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. In this particular
case we have highlighted and selected # 5 on this SEARCH RESULTS page. The
annotation for this probe set mentions that it targets the last three exons
and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span
style="mso-spacerun: yes"> </span>That is just what we want.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. Most probe sets have
not been annotated in as much detail as App. Refer tot the FAQ to learn how
to annotate probe sets yourself.</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/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png Binary files differdeleted file mode 100755 index 08c136e3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png Binary files differdeleted file mode 100755 index b8e67f4d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm deleted file mode 100755 index f7336dcc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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>RESULTS OF THE APP
SEARCH.<span style="mso-spacerun: yes"> </span>A search of the INIA
Brain database generates 18 matches, 10 of which are shown above. The
GeneNetwork will display several hundred matches in pages of 40 each. If a
search generates a larger numbers of hits, then you will need to refine
search terms.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>1. APP is a great
transcript to introduce you to the complexity and power of new array
platforms that often provide ÒalternativeÓ expression estimates for single
genes. There are seven probe sets that target different parts of the APP
transcript. Which of the alternative measurements is most appropriate and
informative? Have a look at the FAQ page for more on this topic, but general
advice: 1. be skeptical and try to validate that the correct transcript and
gene is being measured; 2. check what part of the transcript is complementary
to the probes; 3. evaluate the performance of individual probes based on
expression level, signal-to-noise and other error terms such as the standard
deviation and error.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>2. In this particular
case we have highlighted and selected # 5 on this SEARCH RESULTS page. The
annotation for this probe set mentions that it targets the last three exons
and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span
style="mso-spacerun: yes"> </span>That is just what we want.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>3. Most probe sets have
not been annotated in as much detail as App. Refer tot the FAQ to learn how
to annotate probe sets yourself.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005.htm deleted file mode 100755 index 53f61532..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img
border=0 src="slide0005_image013.png" style='position:absolute;top:8.83%;
left:2.51%;width:77.48%;height:80.56%'>
<div style='position:absolute;top:1.06%;left:0%;width:108.21%;height:8.3%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;
mso-text-indent-alt:56;position:absolute;top:0%;left:1.83%;width:98.16%;
height:78.72%'><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'>First page of data: The
Trait Data and Analysis Form</span><span style='font-size:106%;color:#E9EB5D;
mso-color-index:3;mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<img border=0 src="slide0005_image014.png" style='position:absolute;top:34.98%;
left:68.74%;width:16.42%;height:9.71%'>
<div style='position:absolute;top:23.32%;left:84.76%;width:16.68%;height:34.09%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=O style='position:absolute;top:2.07%;left:6.34%;width:93.65%;
height:95.33%'><span style='position:absolute;top:0%;left:0%;width:90.67%'><span
style='font-size:200%;color:#E9EB5D'><i>Click </i></span></span><span
style='position:absolute;top:16.3%;left:0%;width:90.67%'><span
style='font-size:200%;color:#E9EB5D'><i>here<br>
</i></span></span>
<div style='position:absolute;top:33.15%;left:0%;width:100.0%;height:16.84%'><span
style='font-size:200%;color:#E9EB5D'><i>to learn<br>
</i></span></div>
<div style='position:absolute;top:49.45%;left:0%;width:90.67%;height:16.84%'><span
style='font-size:200%;color:#E9EB5D'><i>about<br>
</i></span></div>
<div style='position:absolute;top:66.3%;left:0%;width:90.67%;height:16.84%'><span
style='font-size:200%;color:#E9EB5D'><i>data<br>
</i></span></div>
<div style='position:absolute;top:83.15%;left:0%;width:90.67%;height:16.84%'><span
style='font-size:200%;color:#E9EB5D'><i>source</i></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>The Trait Data and
Analysis Form is the single most important page from the point of view of
working with GeneNetwork 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>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>1. What is this
database? It is called INIA Brain mRNA M430 (Apr05) PDNN, but what does that
actually mean. How much of the brain was used? How were the animals
processed? Most of these types of questions can be answered by clicking on
the DATABASE link.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. Transcript/gene
LOCATION data is usually from the most recent assembly. You can VERIFY the
location of the probes and probe set using the two VERIFY buttons. VERIFY
UCSC performs a sequence alignment (BLAT analysis) of the probes to the most
recent assembly.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. The PROBE TOOL button
provides you with highly detailed information on the probe sequences used to
assemble the probe set. For example, in this case you can find out which
probes correspond to which of the three exons. You can also review the
performance of the individual probes. Please check the GLOSSARY for
additional details on probes.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>4. The identifiers (IDs)
provide links to other key resources.</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>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png Binary files differdeleted file mode 100755 index 55769e36..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png Binary files differdeleted file mode 100755 index e49ba16e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm deleted file mode 100755 index fbe8c631..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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
Analysis Form is the single most important page from the point of view of
working with GeneNetwork 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>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>1. What is this
database? It is called INIA Brain mRNA M430 (Apr05) PDNN, but what does that
actually mean. How much of the brain was used? How were the animals
processed? Most of these types of questions can be answered by clicking on
the DATABASE link.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>2. Transcript/gene
LOCATION data is usually from the most recent assembly. You can VERIFY the
location of the probes and probe set using the two VERIFY buttons. VERIFY
UCSC performs a sequence alignment (BLAT analysis) of the probes to the most
recent assembly.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>3. The PROBE TOOL button
provides you with highly detailed information on the probe sequences used to
assemble the probe set. For example, in this case you can find out which
probes correspond to which of the three exons. You can also review the
performance of the individual probes. Please check the GLOSSARY for
additional details on probes.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>4. The identifiers (IDs)
provide links to other key resources.</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/html/webqtl_demo2_part1.ppt_files/slide0006.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006.htm deleted file mode 100755 index fa44d20c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<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.png" 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:0%;width:100.26%;height:10.07%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;
mso-text-indent-alt:56;position:absolute;top:0%;left:1.98%;width:96.82%;
height:73.68%'><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: Metadata
for each resource</span></div>
</div>
<img border=0 src="slide0006_image015.png" style='position:absolute;top:6.71%;
left:3.31%;width:60.39%;height:92.22%'></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>Most of the database
components and resources in The GeneNetwork are linked to metadata pages that
provide a human-readable summary of how, why, where, when, and with whom the
data were generated. Before you get too involved with a data set, it is
naturally important to read this information. While the data in The
GeneNetwork may be accessible and useful, that does not always mean that the
data is public domain and available for you to use in publication or for
profit purposes. If you want to know more about the data ownership and usage,
please read through the POLICIES pop-down menu items.</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/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png Binary files differdeleted file mode 100755 index ff7d776a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm deleted file mode 100755 index f29819ad..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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>Most of the database
components and resources in The GeneNetwork are linked to metadata pages that
provide a human-readable summary of how, why, where, when, and with whom the
data were generated. Before you get too involved with a data set, it is
naturally important to read this information. While the data in The
GeneNetwork may be accessible and useful, that does not always mean that the
data is public domain and available for you to use in publication or for
profit purposes. If you want to know more about the data ownership and usage,
please read through the POLICIES pop-down menu items.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007.htm deleted file mode 100755 index a30b21f1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:-.35%;left:-.79%;width:109.13%;height:7.42%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;
mso-text-indent-alt:56;position:absolute;top:0%;left:1.82%;width:98.17%;
height:88.09%'><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'>Expression estimates for </span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'> on the Trait Data form</span><span
style='font-size:81%;color:#E9EB5D;mso-color-index:3'> </span></div>
</div>
<div style='position:absolute;top:81.09%;left:2.51%;width:110.46%;height:11.48%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:7.69%;left:.83%;width:99.16%;
height:84.61%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:183%;color:#E9EB5D;mso-color-index:
3'>Trait data for each strain with SE when known. For array data the scale is </span></span><span
style='position:absolute;top:49.09%;left:0%;width:84.28%'><span
style='font-family:"Gill Sans";font-size:183%;color:#E9EB5D;mso-color-index:
3'>~ log base 2.<span style="mso-spacerun: yes"> </span></span><span
style='font-size:167%;color:#E9EB5D;mso-color-index:3'>F1 data = 16.723 =
2^16.723 = 108,174</span></span></div>
</div>
<img border=0 src="slide0007_image016.png" style='position:absolute;top:7.77%;
left:2.51%;width:51.65%;height:72.26%'><img border=0
src="slide0007_image017.png" style='position:absolute;top:33.92%;left:57.88%;
width:30.72%;height:13.42%'>
<div style='position:absolute;top:47.7%;left:57.48%;width:36.29%;height:18.9%;
filter:DropShadow(Color=#000000, OffX=2, OffY=1)'>
<div class=O style='position:absolute;top:3.73%;left:2.91%;width:97.08%;
height:96.26%'><span style='position:absolute;top:0%;left:0%;width:96.24%'><span
style='font-size:167%;color:#E9EB5D;mso-color-index:3'>These values can all </span></span><span
style='position:absolute;top:25.24%;left:0%;width:93.98%'><span
style='font-size:167%;color:#E9EB5D;mso-color-index:3'>be changed by the </span></span><span
style='position:absolute;top:49.51%;left:0%;width:100.0%'><span
style='font-size:167%;color:#E9EB5D;mso-color-index:3'>user. (Yes, there is a </span></span><span
style='position:absolute;top:74.75%;left:0%;width:93.98%'><span
style='font-size:167%;color:#E9EB5D;mso-color-index:3'>RESET)</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=Helvetica size=3>This slide shows you the
lower parts of the Trait Data and Analysis Form with the data for the first
set of BXD strains</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/html/webqtl_demo2_part1.ppt_files/slide0007_image016.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image016.png Binary files differdeleted file mode 100755 index 53a17c76..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image016.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image017.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image017.png Binary files differdeleted file mode 100755 index 308c4df0..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image017.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_notes_pane.htm deleted file mode 100755 index f5bc813e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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 shows you the
lower parts of the Trait Data and Analysis Form with the data for the first
set of BXD strains</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008.htm deleted file mode 100755 index c0fa9166..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:.53%;left:.79%;width:98.54%;height:8.12%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;
mso-text-indent-alt:56;position:absolute;top:0%;left:2.01%;width:96.9%;
height:91.3%'><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'>Critiquing 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'> data the Trait Data</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:74.38%;left:2.51%;width:110.86%;height:13.78%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=O style='position:absolute;top:6.41%;left:.83%;width:99.16%;
height:88.46%'><span style='position:absolute;top:0%;left:0%;width:98.55%'><span
style='font-family:"Gill Sans";font-size:150%;color:#E9EB5D;mso-color-index:
3'>Use the BASIC STATISTICS button to evaluate the App data. You will find that
App data </span></span><span style='position:absolute;top:31.88%;left:0%;
width:100.0%'><span style='font-family:"Gill Sans";font-size:150%;color:#E9EB5D;
mso-color-index:3'>from the different strains are not equally trustworthy. BXD8
is an obvious outlier without </span></span><span style='position:absolute;
top:63.76%;left:0%;width:93.85%'><span style='font-family:"Gill Sans";
font-size:150%;color:#E9EB5D;mso-color-index:3'>replication (no error bar)</span><span
style='font-size:150%;color:#E9EB5D;mso-color-index:3'>. BXD33 is also
suspiciously low. BXD5 is noisy. </span><span style='font-family:"Gill Sans";
font-size:150%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></span></div>
</div>
<img border=0 src="slide0008_image018.png" style='position:absolute;top:7.77%;
left:2.11%;width:16.02%;height:18.72%'><img border=0
src="slide0008_image019.png" style='position:absolute;top:8.3%;left:18.27%;
width:73.37%;height:66.07%'><img border=0 src="slide0008_image021.png"
style='position:absolute;top:87.27%;left:59.6%;width:30.72%;height:13.42%'></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 Basic Statistics
page allows you to evaluate some aspects of the data quality. In this case,
BXD8 is a potential problem. An outlier of this type may be generated by a
technical artifact (bad sample?). However, it is also possible that BXD8 just
has genuine low endogenous expression of App and may therefore be a
particularly valuable model for research. There are different ways to treat
problematic data of these types. One way is simply to discard this datum. The
other way is to prevent outliers from have too much influence quantitatively,
while leaving them in their low (or high positions). This is called
windsorizing the data (after King Henry the VIII who had a habit of chopping
heads). In this case, we have windsorized the BXD8 to a value of 16.0 and the
BXD33 to a value of 16.02. Rank is retained. We are making a bet that the two
lowest strains are really low, but we are hedging our bet and just making
them a little lower than BXD90. This removes their ÒundueÓ influence.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>1. It turns out that
BXD8 is a strain with many odd phenotypes. The whole strain is essentially an
outlier for many traits. Therefore, the low App expression data may be quite
accurate. Still, it would be comforting to have at least two more replicates.</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/html/webqtl_demo2_part1.ppt_files/slide0008_image018.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image018.png Binary files differdeleted file mode 100755 index 9535e6bb..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image018.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image019.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image019.png Binary files differdeleted file mode 100755 index 7e86d735..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image019.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image021.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image021.png Binary files differdeleted file mode 100755 index 2f8dfb0a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image021.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm deleted file mode 100755 index 455928c7..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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 Basic Statistics
page allows you to evaluate some aspects of the data quality. In this case,
BXD8 is a potential problem. An outlier of this type may be generated by a
technical artifact (bad sample?). However, it is also possible that BXD8 just
has genuine low endogenous expression of App and may therefore be a
particularly valuable model for research. There are different ways to treat
problematic data of these types. One way is simply to discard this datum. The
other way is to prevent outliers from have too much influence quantitatively,
while leaving them in their low (or high positions). This is called
windsorizing the data (after King Henry the VIII who had a habit of chopping
heads). In this case, we have windsorized the BXD8 to a value of 16.0 and the
BXD33 to a value of 16.02. Rank is retained. We are making a bet that the two
lowest strains are really low, but we are hedging our bet and just making
them a little lower than BXD90. This removes their ÒundueÓ influence.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>1. It turns out that
BXD8 is a strain with many odd phenotypes. The whole strain is essentially an
outlier for many traits. Therefore, the low App expression data may be quite
accurate. Still, it would be comforting to have at least two more replicates.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009.htm deleted file mode 100755 index 2daff7ac..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009.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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:0%;left:1.72%;width:93.64%;height:14.48%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;
mso-text-indent-alt:56;position:absolute;top:0%;left:2.12%;width:96.6%;
height:51.21%'><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'><i>App</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> expression after
windsorizing</span></div>
</div>
<img border=0 src="slide0009_image022.png" style='position:absolute;top:8.83%;
left:2.51%;width:94.17%;height:83.74%'></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>Now we get a much better
feel for the variation in the error among the cases. Those without error bars
are of course the ÒnoisiestÓ of all. This data set is not complete yet (the
aim is to acquire at least one male-female sample for each BXD strain).</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/html/webqtl_demo2_part1.ppt_files/slide0009_image022.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_image022.png Binary files differdeleted file mode 100755 index e03c35ed..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_image022.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_notes_pane.htm deleted file mode 100755 index b2f9f9f2..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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>Now we get a much better
feel for the variation in the error among the cases. Those without error bars
are of course the ÒnoisiestÓ of all. This data set is not complete yet (the
aim is to acquire at least one male-female sample for each BXD strain).</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010.htm deleted file mode 100755 index 4d02c34e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010.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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
<!--.sld
{left:0px !important;
width:6.0in !important;
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:0%;left:.79%;width:93.64%;height:14.48%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;
mso-text-indent-alt:56;position:absolute;top:0%;left:2.12%;width:97.45%;
height:51.21%'><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="slide0010_image023.png" style='position:absolute;top:10.07%;
left:3.31%;width:94.17%;height:37.27%'><img border=0
src="slide0010_image024.png" style='position:absolute;top:38.86%;left:61.72%;
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 this
particular App transcript steady-state abundance level correlate with those
of any other transcripts in the same INIA Brain mRNA M430 data set?</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>You can CHOOSE many other DATABASES at this point if
you want, but for now letÕs stick with the default.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. There are different
ways to sort the correlations. The most obvious is by p-value (most
significant values at the top of the list), but it is also interesting to
sort the top 100 or top 500 by their gene symbol (gene ID) or by their
chromosomal location (position).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. If you donÕt want
your analysis to be sensitive to outliers, then you may want to choose to use
the Spearman Rank Order method of calculating correlations.</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/html/webqtl_demo2_part1.ppt_files/slide0010_image023.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image023.png Binary files differdeleted file mode 100755 index 1d32d035..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image023.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image024.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image024.png Binary files differdeleted file mode 100755 index 152e5045..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image024.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_notes_pane.htm deleted file mode 100755 index 3d3f0e48..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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 this
particular App transcript steady-state abundance level correlate with those
of any other transcripts in the same INIA Brain mRNA M430 data set?</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font
face=Helvetica size=2>You can CHOOSE many other DATABASES at this point if
you want, but for now letÕs stick with the default.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>2. There are different
ways to sort the correlations. The most obvious is by p-value (most
significant values at the top of the list), but it is also interesting to
sort the top 100 or top 500 by their gene symbol (gene ID) or by their
chromosomal location (position).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>3. If you donÕt want
your analysis to be sensitive to outliers, then you may want to choose to use
the Spearman Rank Order method of calculating correlations.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011.htm deleted file mode 100755 index 362057fc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011.htm +++ /dev/null @@ -1,25 +0,0 @@ -<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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:.35%;left:-.79%;width:93.64%;height:14.48%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;
mso-text-indent-alt:56;position:absolute;top:0%;left:2.12%;width:96.6%;
height:51.21%'><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'>Transcript neighborhoods</span></div>
</div>
<img border=0 src="slide0011_image025.png" style='position:absolute;top:7.77%;
left:2.51%;width:85.82%;height:91.87%'></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 Traits Correlation
output window (Correlation Results) compares App expression data with all
other traits in this INIA Brain data set. The most significant 100 or 500
transcripts are sorted by their p-values. The top correlation is that of the
probe set to itself (often a value of 1.0, but in this case we modified the
App values manually by windsorizing the data). The next best correlation is
to another App probe set. The fourth correlation is interesting and suggests
that there may be a link between App and a particular type of ataxia (Atcay).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>Use the checkboxes to the far left to select traits
that you want to study together. Once you have selected interesting traits,
click on the ADD SELECTION button. This puts all of the selected traits into
a SELECTIONS WINDOW for other types of analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. The p-value is not
corrected for multiple tests. A conservative approach for array data would be
to assume 10,000 nominally independent tests. Subtract 4 from the exponent
and if the value is still smaller than 0.05 you may have a real correlation.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. The LITERATURE
CORRELATION is a data type generated by Drs. Ramin Homayouni and Michael
Berry. Click on the header column by the asterisk for more information on
this highly useful data type.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>4. We are using Pearson
product moment correlations rather that the Spearman rank order correlation.
But you can select either in the previous step.</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/html/webqtl_demo2_part1.ppt_files/slide0011_image025.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_image025.png Binary files differdeleted file mode 100755 index d29a333f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_image025.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm deleted file mode 100755 index 1f0dd0d1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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 Traits Correlation
output window (Correlation Results) compares App expression data with all
other traits in this INIA Brain data set. The most significant 100 or 500
transcripts are sorted by their p-values. The top correlation is that of the
probe set to itself (often a value of 1.0, but in this case we modified the
App values manually by windsorizing the data). The next best correlation is
to another App probe set. The fourth correlation is interesting and suggests
that there may be a link between App and a particular type of ataxia (Atcay).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font
face=Helvetica size=2>Use the checkboxes to the far left to select traits
that you want to study together. Once you have selected interesting traits,
click on the ADD SELECTION button. This puts all of the selected traits into
a SELECTIONS WINDOW for other types of analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>2. The p-value is not
corrected for multiple tests. A conservative approach for array data would be
to assume 10,000 nominally independent tests. Subtract 4 from the exponent
and if the value is still smaller than 0.05 you may have a real correlation.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>3. The LITERATURE
CORRELATION is a data type generated by Drs. Ramin Homayouni and Michael
Berry. Click on the header column by the asterisk for more information on
this highly useful data type.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>4. We are using Pearson
product moment correlations rather that the Spearman rank order correlation.
But you can select either in the previous step.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012.htm deleted file mode 100755 index 4f1cf425..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:.35%;left:1.72%;width:93.64%;height:14.48%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;
mso-text-indent-alt:56;position:absolute;top:0%;left:2.12%;width:96.6%;
height:51.21%'><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'><i>App</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> and </span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>Atcay</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript scatterplot </span></div>
</div>
<img border=0 src="slide0012_image026.png" style='position:absolute;top:8.48%;
left:5.03%;width:66.22%;height:91.16%'></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>By clicking on the
CORRELATION of the Atcay transcript to the App transcript, you can generate a
Correlation plot between these two transcripts. In this App and Atcay
scatterplot, each point is a strain mean value. For example, BXD33 and BXD8
have low App and Atcay expressions. The two parental strains and the F1 are
also included in this plot.</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/html/webqtl_demo2_part1.ppt_files/slide0012_image026.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_image026.png Binary files differdeleted file mode 100755 index a0675ffc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_image026.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_notes_pane.htm deleted file mode 100755 index c13d07ec..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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>By clicking on the
CORRELATION of the Atcay transcript to the App transcript, you can generate a
Correlation plot between these two transcripts. In this App and Atcay
scatterplot, each point is a strain mean value. For example, BXD33 and BXD8
have low App and Atcay expressions. The two parental strains and the F1 are
also included in this plot.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013.htm deleted file mode 100755 index 5aa623bf..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013.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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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{left:0px !important;
width:6.0in !important;
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font-size:76% !important;}
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--
-gId="slide0013.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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:.35%;left:.79%;width:99.47%;height:14.48%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;
mso-text-indent-alt:56;position:absolute;top:0%;left:1.99%;width:96.8%;
height:51.21%'><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'><i>App</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript and eight of
its neighbors</span></div>
</div>
<img border=0 src="slide0013_image027.png" style='position:absolute;top:9.71%;
left:2.51%;width:83.84%;height:90.1%'></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>A group of traits from
many different databases can be selected and brought together for joint
analysis. In this case all of the content of the BXD SELECTIONS is from a
single BRAIN database, the top 20 neighbors of the App transcript from the
Correlation Results table. Eight of these neighbors plus App is shown in the
slide.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>All of items in the BXD SELECTIONS were selected using
the SELECT ALL button</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. The buttons at the
top (and bottom) of this page can do some cool stuff. We will work with
NETWORK GRAPH first.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. Think of the
SELECTIONS as your shopping cart. You go to different aisles in the
supermarket to acquire different types of items of interest. These could
include transcripts, classical phenotypes (longevity, brain weight, prepulse
inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves
doing some analysis with the items in the cart.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>4. Different tools
handle different numbers of items. Most will handle up to 100 traits.</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>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_image027.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_image027.png Binary files differdeleted file mode 100755 index ba473846..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_image027.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm deleted file mode 100755 index 4d56b194..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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>A group of traits from
many different databases can be selected and brought together for joint
analysis. In this case all of the content of the BXD SELECTIONS is from a
single BRAIN database, the top 20 neighbors of the App transcript from the
Correlation Results table. Eight of these neighbors plus App is shown in the
slide.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font
face=Helvetica size=2>All of items in the BXD SELECTIONS were selected using
the SELECT ALL button</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>2. The buttons at the
top (and bottom) of this page can do some cool stuff. We will work with
NETWORK GRAPH first.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>3. Think of the
SELECTIONS as your shopping cart. You go to different aisles in the
supermarket to acquire different types of items of interest. These could
include transcripts, classical phenotypes (longevity, brain weight, prepulse
inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves
doing some analysis with the items in the cart.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>4. Different tools
handle different numbers of items. Most will handle up to 100 traits.</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/html/webqtl_demo2_part1.ppt_files/slide0014.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014.htm deleted file mode 100755 index 156a5132..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014.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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description
content="Aug-15-05: App transcript coexpression neighborhood">
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:82.15%;left:4.1%;width:96.15%;height:18.19%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div>
<div style='position:absolute;top:-2.29%;left:.79%;width:105.43%;height:12.54%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='position:absolute;top:19.71%;left:1.25%;width:98.74%;
height:61.97%'><span style='font-size:82%'><i>App</i></span><span
style='font-size:82%'> transcript coexpression neighborhood</span><span
style='mso-special-format:lastCR;display:none'><br>
</span></div>
</div>
<img border=0 src="slide0014_image029.png" style='position:absolute;top:37.8%;
left:1.72%;width:97.48%;height:62.19%'><img border=0
src="slide0014_image031.png" style='position:absolute;top:11.13%;left:1.72%;
width:79.47%;height:25.44%'><img border=0 src="slide0014_image033.png"
style='position:absolute;top:10.6%;left:81.32%;width:18.8%;height:9.89%'></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>Output of the Network
Graph. Warm colors (orange and red) are positive correlations above 0.5
whereas cool colors (green and blue) are negative correlations. Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3> All of the nodes (gene/transcripts) on this graph are
clickable.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. For this graph the
App expression values have ÒrevertedÓ to their pre-Windsorized values.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. To generate this
graph, we used the default setting:<span style="mso-spacerun: yes">
</span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use
curved lines (aka ÒedgesÓ).</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/html/webqtl_demo2_part1.ppt_files/slide0014_image029.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image029.png Binary files differdeleted file mode 100755 index 8f560834..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image029.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image031.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image031.png Binary files differdeleted file mode 100755 index 8d72b4c1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image031.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image033.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image033.png Binary files differdeleted file mode 100755 index c1cd1c01..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image033.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm deleted file mode 100755 index 728a1a82..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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>Output of the Network
Graph. Warm colors (orange and red) are positive correlations above 0.5
whereas cool colors (green and blue) are negative correlations. Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font
face=Helvetica size=2> All of the nodes (gene/transcripts) on this graph are
clickable.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>2. For this graph the
App expression values have ÒrevertedÓ to their pre-Windsorized values.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>3. To generate this
graph, we used the default setting:<span style="mso-spacerun: yes">
</span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use
curved lines (aka ÒedgesÓ).</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015.htm deleted file mode 100755 index c2a26be3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015.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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:0%;left:.79%;width:93.64%;height:14.48%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292;
mso-text-indent-alt:0;position:absolute;top:0%;left:1.13%;width:97.59%;
height:51.21%'><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'>Correlations of </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'> with classical traits</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
<img border=0 src="slide0015_image034.png" style='position:absolute;top:28.97%;
left:4.1%;width:78.27%;height:70.84%'><img border=0 src="slide0015_image035.png"
style='position:absolute;top:8.12%;left:4.1%;width:33.5%;height:19.61%'></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>Going back to the Trait
Data and Analysis Form window, we have computed the correlations between
strain variation in App expression level and other classical phenotypes that
have already been measured in many of the same BXD strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>The number of common strains varies widely--in this
case from 14 to 23 strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. We can add these
traits (four are selected) to our BXD SELECTIONS window.</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/html/webqtl_demo2_part1.ppt_files/slide0015_image034.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image034.png Binary files differdeleted file mode 100755 index dafa2898..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image034.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image035.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image035.png Binary files differdeleted file mode 100755 index 35566d47..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image035.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm deleted file mode 100755 index 373646fe..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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>Going back to the Trait
Data and Analysis Form window, we have computed the correlations between
strain variation in App expression level and other classical phenotypes that
have already been measured in many of the same BXD strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=2>1.</font><font
face=Helvetica size=2>The number of common strains varies widely--in this
case from 14 to 23 strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>2. We can add these
traits (four are selected) to our BXD SELECTIONS window.</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016.htm deleted file mode 100755 index 9432ca4c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016.htm +++ /dev/null @@ -1,25 +0,0 @@ -<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 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<link rel=Stylesheet href="master03_stylesheet.css">
<style media=print>
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{left:0px !important;
width:6.0in !important;
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font-size:76% !important;}
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<script language=JavaScript src=script.js></script><script language=JavaScript><!--
-gId="slide0016.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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-</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.png" v:shapes="_x0000_s1026"
style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:0%;left:.79%;width:99.47%;height:10.24%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292;
mso-text-indent-alt:0;position:absolute;top:0%;left:1.06%;width:98.66%;
height:72.41%'><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'>Network Graph of </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'> with classical traits</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
<img border=0 src="slide0016_image036.png" style='position:absolute;top:8.3%;
left:3.31%;width:88.21%;height:90.63%'></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 have computed the
Network Graph, now using other types of traits.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Saline Hot Plate Latency
is the green node labeled 10020.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Freezing (fear) is the
green node labeled 10447.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</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/html/webqtl_demo2_part1.ppt_files/slide0016_image036.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_image036.png Binary files differdeleted file mode 100755 index baa1d807..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_image036.png +++ /dev/null diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_notes_pane.htm deleted file mode 100755 index c2a078c5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.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 have computed the
Network Graph, now using other types of traits.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Saline Hot Plate Latency
is the green node labeled 10020.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Freezing (fear) is the
green node labeled 10447.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br>
</td>
</tr>
</table>
</body>
</html>
\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0017.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0017.htm deleted file mode 100755 index afb498b8..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0017.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
<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.png" 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:93.64%;height:14.48%;
filter:DropShadow(Color=#000000, OffX=1, OffY=1)'>
<div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292;
mso-text-indent-alt:0;position:absolute;top:0%;left:1.13%;width:97.59%;
height:51.21%'><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'>Summary of Part 1:</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</div>
<div style='position:absolute;top:10.77%;left:8.47%;width:100.79%;height:47.87%'>
<div class=O1 style='mso-margin-left-alt:432'></div>
<div class=O2 style='mso-margin-left-alt:720'></div>
<div class=O3 style='mso-margin-left-alt:1008'></div>
<div class=O4 style='mso-margin-left-alt:1296'></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:0%;
left:0%;width:90.14%;height:11.07%'><span style='position:absolute;top:0%;
left:2.76%;width:97.23%'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.84%;font-family:Arial'>1.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You have learned the basics
about searching for traits<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:11.43%;
left:0%;width:84.88%;height:11.07%'><span style='position:absolute;top:0%;
left:2.94%;width:97.05%'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-3.03%;font-family:Arial'>2.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know some methods to check
data quality<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:22.5%;
left:0%;width:84.88%;height:11.07%'><span style='position:absolute;top:0%;
left:2.94%;width:97.05%'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-3.03%;font-family:Arial'>3.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to edit bad or
suspicious data<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:33.57%;
left:0%;width:90.01%;height:11.07%'><span style='position:absolute;top:0%;
left:2.77%;width:97.22%'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.85%;font-family:Arial'>4.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to review the
basic statistics of a trait<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:44.64%;
left:0%;width:93.56%;height:22.14%'><span style='position:absolute;top:0%;
left:2.66%;width:97.33%'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.74%;font-family:Arial'>5.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to generate a
scattergram between two </span></span><span style='position:absolute;
top:50.0%;left:2.66%;width:88.06%'><span style='font-family:"Gill Sans";
font-size:200%;color:#E9EB5D;mso-color-index:3'>traits using the Traits
Correlation tool<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:66.78%;
left:0%;width:100.0%;height:11.07%'><span style='position:absolute;top:0%;
left:2.49%;width:97.5%'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.56%;font-family:Arial'>6.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to add items to
your SELECTIONS window<br>
</span></span></div>
<div class=O style='mso-margin-left-alt:144;position:absolute;top:77.85%;
left:0%;width:99.34%;height:22.14%'><span style='position:absolute;top:0%;
left:2.51%;width:97.48%'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1";
position:absolute;left:-2.57%;font-family:Arial'>7.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to generate a
Network Graph of traits that </span></span><span style='position:absolute;
top:51.66%;left:2.51%;width:82.93%'><span style='font-family:"Gill Sans";
font-size:200%;color:#E9EB5D;mso-color-index:3'>co-vary. </span></span></div>
</div>
<div class=O style='position:absolute;top:67.31%;left:5.96%;width:105.29%;
height:26.5%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'>What does genetic covariance mean? The genetic covariance can </span></span><span
style='position:absolute;top:20.0%;left:0%;width:96.1%'><span style='font-family:
"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:3'>be functional and
mechanistic, but it can also be due to linkage </span></span><span
style='position:absolute;top:40.0%;left:0%;width:95.97%'><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'>disequilibrium. Finally, it can be due to sampling error or poor </span></span><span
style='position:absolute;top:60.66%;left:0%;width:87.92%'><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'>experimental design. Evaluate the biological plausibility of </span></span><span
style='position:absolute;top:80.66%;left:0%;width:85.28%'><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'>correlations. Test and be skeptical.</span></span></div>
</div>
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genomics</title>
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style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'>
<div style='position:absolute;top:2.29%;left:2.51%;width:94.43%;height:9.89%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:19.64%;
left:1.4%;width:97.47%;height:69.64%'><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:16.6%;left:6.62%;width:90.19%;height:24.38%;
filter:DropShadow(Color=#000000, OffX=2, OffY=2)'>
<div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:0%;
left:1.46%;width:97.35%;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:34.05%;left:4.67%;width:95.47%'><span
style='font-size:82%'><br>
</span></span><span style='position:absolute;
top:68.11%;left:4.67%;width:95.47%'><span style='font-size:82%;mso-special-format:
lastCR;display:none'><br>
</span></span></div>
</div>
<div class=O style='position:absolute;top:27.56%;left:9.4%;width:50.59%;
height:7.77%'><span style='font-family:"Gill Sans";font-size:300%;color:#E9EB5D'>kmanly@utmem.edu</span></div>
<div class=O style='position:absolute;top:83.56%;left:4.37%;width:108.34%;
height:15.9%'><span style='position:absolute;top:0%;left:0%;width:90.83%'><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'>The </span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'><i>App</i></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D'> findings reviewed
in this presentation are part of an </span></span><span style='position:absolute;
top:33.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";
font-size:200%;color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and
R. Clark (July 15, </span></span><span style='position:absolute;top:66.66%;
left:0%;width:84.35%'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D'>2005)</span><span style='font-family:"Gill Sans";font-size:300%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><br>
</span></span></div>
</div>
<div id=NotesObj style='display:none'>
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<td width=5 nowrap></td>
<td width="100%"></td>
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<td align=left colspan=1><font face=Verdana size=3>END</font><br>
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<head>
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<td align=left colspan=1><font face=Verdana size=2>END</font><br>
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mso-text-indent-alt:0;mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232;
mso-text-indent-alt:0'><span style='font-size:105%'><i>GeneNetwork and WebQTL:</i></span><span
style='font-size:68%;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
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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'>Part 1: How to study </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.57 * 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:106%;color:#E9EB5D;mso-color-index:
3'>covariation (slides 2–16)<br>
</span></span></layer></div>
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<div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt:
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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'>Part 2. Discovering
upstream </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.59 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index:
3'>modulators (slides 17–30)</span><span style='font-size:94%;color:#E9EB5D;
mso-color-index:3;mso-special-format:lastCR;display:none'><br>
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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:
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<div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E;
display:none'><br>
</span></div>
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<div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt:
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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-family:"Gill Sans";font-size:217%;
color:#E9EB5D;mso-color-index:3'><i>PowerPoint ÒNormal viewÓ has notes that may
be </i></span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.69 * 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'><i>useful companions to these slides.</i></span><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3;mso-special-format:lastCR;display:none'><br>
</span></span></layer></div>
</layer><script> - mytop = 0.1 * g_height; myleft = 0.06 * g_width; myheight = 0.07 * g_height; mywidth = 0.55 * 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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color:#E9EB5D'><i>a PowerPoint Presentation</i></span><span style='font-family:
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none'><i><br>
</i></span></div>
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<div style='text-align:left;font-family:Verdana;font-weight:normal;font-style:
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color:#E9EB5D'><i>RWW 07.23.2005</i></span></div>
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
mso-color-index:3'><i>You can also download this PowerPoint at<br>
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<div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;
mso-color-index:3'><i>ftp://atlas.utmem.edu/public/webqtl_demo2.ppt </i></span><span
style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:
3;mso-special-format:lastCR;display:none'><br>
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</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=Helvetica size=3>Welcome to a short
demonstration of the GeneNetwork and its WebQTL module. Please adjust the
size of the windows on your monitor so that you can see part of this page,
as well as GeneNetwork windows. WebQTL produces a large number of new
windows, so you may need to modify your browser preferences to permit
pop-ups. In this demonstration, we explore one important transcript
expressed in the brain: the amyloid beta precursor protein messenger RNA. A
protein product of this mRNA, the APP protein, is associated with
AlzheimerÕs 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>My thanks to Dr. Robert
F. Clark and Wenli Cai for testing this PowerPoint demonstration and making
many improvements.</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. Edits July 13, 2005 by RW and RFC. Edit July 14,
2005 by WC. Final edits by RF Clark, July 22, 2005.</font><br>
</td>
</tr>
</table>
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<td align=left colspan=1><font face=Verdana size=2>END</font><br>
</td>
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<div style='mso-line-spacing:"-224 0 0"'><span style='font-family:"Gill Sans";
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<div style='mso-line-spacing:"-224 0 0"'><span style='font-family:"Gill Sans";
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<div style='mso-line-spacing:"-224 0 0"'><span style='font-family:"Gill Sans";
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3;mso-special-format:lastCR;display:none'><i><br>
</i></span></div>
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<div>
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mso-text-raise:0%'></div>
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<script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 1.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:nobullet;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%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
348;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";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'>PART 1: How to study
variation and covariation</span></div>
</layer></div>
</layer></div>
</layer><script> - mytop = 0.15 * g_height; myleft = 0.85 * g_width; myheight = 0.22 * g_height; mywidth = 0.16 * 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 = 0.21 * g_height; mywidth = 0.15 * 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:"-224 0 0";mso-line-spacing:"-224 0 0"'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * 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'>Choose<span style="mso-spacerun: yes">
</span></span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * 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'>species, </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * 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'>group, </span></span></layer><script> - mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * 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'>and type</span></span></layer></div>
</layer></div>
</layer><script> - mytop = 0.71 * g_height; myleft = 0.48 * g_width; myheight = 0.13 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
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-
<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>Please link to the web
site:<span style="mso-spacerun: yes">
</span>http://www.genenetwork.org</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>To begin a search you
make choices about what species, group, and database to explore.</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>For this demonstration
enter APP as above and click on the SEARCH button. Make sure that the
DEFAULT SETTINGS are species = Mouse, Group = BXD, Type = Whole Brain, and
Database = INIA BRAIN mRNA M430 (Apr05) PDNN.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>1. The GeneNetwork and
WebQTL are often used to work with public data sets. However, it is possible
to enter and analyze your own data for specific genetic reference
populations such as the BXD genetic reference population of mice or the HXB
strains of rat. Entering your own data is a more advanced topic, but if you
click on the HOME pop-down menu (upper left), you will see ÒEnter Trait
DataÓ that will explain the process.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>2.</font><font
face=Helvetica size=3> For help on advanced searching methods read the left
side of the page (INTRODUCTION).<span style="mso-spacerun: yes">
</span>If you make a search term too complex, you may get no hits (try
entering Òamyloid betaÓ for example). If you make it too simple, you may
also get too many.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>3.</font><font
face=Helvetica size=3> Use the asterisk * as a wildcard. For example, to
find all <i>Hoxb</i> transcripts, search for Hoxb*.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>4.</font><font
face=Helvetica size=3> In some cases you can also research for transcripts
and genes using special search strings such as Ò</font><font face=Geneva
size=3>Mb = (Chr1, 100 102)Ó to find all genes on Chromosome 1 between 98
and 104 megabases (donÕt actually use the quotes). Details are described at </font><font
face=Verdana size=3>http://www.genenetwork.org/searchHelp.html</font><font
face=Geneva size=3>.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>5.<span
style="mso-spacerun: yes"> </span>These INFO buttons provide
links to data about the different data types. Try them.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>6.<span
style="mso-spacerun: yes"> </span>The SET TO DEFAULT button is used to
change the database default setting to match your typical search categories.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
-</script><script language=JavaScript><!--
-function playList() { - -} -//-->
-</script>
</body>
</html>
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none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Please also use the
Glossary, FAQ, and News</span></div>
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<td align=left colspan=1><font face=Helvetica size=3>SHORT DETOUR to the
HELP menu. If you are new to the GeneNetwork, you may find it helpful to
review the The Glossary and FAQ pages shown above. We are in the process of
making ÒliveÓ demos for some of the key modules in the GeneNetwork. Check
the NEWS every month or two to find out about new features.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><br>
</td>
</tr>
</table>
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color:#E9EB5D;mso-color-index:3'>Highlight </span></span></layer><script> - mytop = 0.05 * 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><span
style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%;
color:#E9EB5D;mso-color-index:3'>this probe </span></span></layer><script> - mytop = 0.1 * 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><span
style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%;
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%;
color:#E9EB5D;mso-color-index:3'>and</span><span style='font-family:"Gill Sans";
font-size:217%;color:#E9EB5D;mso-color-index:3;display:none'><i><br>
</i></span></span></layer></div>
</layer><script> - mytop = 0.2 * g_height; myleft = 0 * g_width; myheight = 0.26 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-line-spacing:"-224 0 0"'><script> - mytop = 0 * 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><span
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%;
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%;
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%;
color:#E9EB5D;mso-color-index:3'>checkbox</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>
</layer></div>
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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%'><span style='font-size:82%'>Search results</span><span
style='mso-special-format:lastCR;display:none'><br>
</span></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>RESULTS OF THE APP
SEARCH.<span style="mso-spacerun: yes"> </span>A search of the INIA
Brain database generates 18 matches, 10 of which are shown above. The
GeneNetwork will display several hundred matches in pages of 40 each. If a
search generates a larger numbers of hits, then you will need to refine
search terms.</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>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>1. APP is a great
transcript to introduce you to the complexity and power of new array
platforms that often provide ÒalternativeÓ expression estimates for single
genes. There are seven probe sets that target different parts of the APP
transcript. Which of the alternative measurements is most appropriate and
informative? Have a look at the FAQ page for more on this topic, but general
advice: 1. be skeptical and try to validate that the correct transcript and
gene is being measured; 2. check what part of the transcript is
complementary to the probes; 3. evaluate the performance of individual
probes based on expression level, signal-to-noise and other error terms such
as the standard deviation and error.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. In this particular
case we have highlighted and selected # 5 on this SEARCH RESULTS page. The
annotation for this probe set mentions that it targets the last three exons
and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span
style="mso-spacerun: yes"> </span>That is just what we want.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. Most probe sets have
not been annotated in as much detail as App. Refer tot the FAQ to learn how
to annotate probe sets yourself.</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/html/webqtl_demo2_part1.ppt_files/slide0023.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm deleted file mode 100755 index 10a6218a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm +++ /dev/null @@ -1,128 +0,0 @@ -<html>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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<div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans";
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display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'>First page of data: The
Trait Data and Analysis Form</span><span style='font-size:106%;color:#E9EB5D;
mso-color-index:3;mso-special-format:lastCR;display:none'><br>
</span></div>
</layer></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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style='text-align:left'><span style='font-size:200%;color:#E9EB5D'><i>here<br>
</i></span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<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>
</layer></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=Helvetica size=3>The Trait Data and
Analysis Form is the single most important page from the point of view of
working with GeneNetwork 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>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>1. What is this
database? It is called INIA Brain mRNA M430 (Apr05) PDNN, but what does that
actually mean. How much of the brain was used? How were the animals
processed? Most of these types of questions can be answered by clicking on
the DATABASE link.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. Transcript/gene
LOCATION data is usually from the most recent assembly. You can VERIFY the
location of the probes and probe set using the two VERIFY buttons. VERIFY
UCSC performs a sequence alignment (BLAT analysis) of the probes to the most
recent assembly.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. The PROBE TOOL
button provides you with highly detailed information on the probe sequences
used to assemble the probe set. For example, in this case you can find out
which probes correspond to which of the three exons. You can also review the
performance of the individual probes. Please check the GLOSSARY for
additional details on probes.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>4. The identifiers
(IDs) provide links to other key resources.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><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/html/webqtl_demo2_part1.ppt_files/slide0024.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0024.htm deleted file mode 100755 index 97f09734..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0024.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html>
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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: Metadata
for each resource</span></div>
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<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Most of the database
components and resources in The GeneNetwork are linked to metadata pages
that provide a human-readable summary of how, why, where, when, and with
whom the data were generated. Before you get too involved with a data set,
it is naturally important to read this information. While the data in The
GeneNetwork may be accessible and useful, that does not always mean that the
data is public domain and available for you to use in publication or for
profit purposes. If you want to know more about the data ownership and
usage, please read through the POLICIES pop-down menu items.</font><br>
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0025.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0025.htm deleted file mode 100755 index 32820d64..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0025.htm +++ /dev/null @@ -1,134 +0,0 @@ -<html>
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<div style='mso-special-format:nobullet;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%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
348;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:94%;color:#E9EB5D;mso-color-index:3'>Expression estimates for </span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3'> on the Trait Data form</span><span
style='font-size:81%;color:#E9EB5D;mso-color-index:3'> </span></div>
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</layer><script> - mytop = 0.81 * g_height; myleft = 0.02 * g_width; myheight = 0.11 * g_height; mywidth = 1.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:183%;
color:#E9EB5D;mso-color-index:3'>Trait data for each strain with SE when known.
For array data the scale is </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * 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:183%;
color:#E9EB5D;mso-color-index:3'>~ log base 2.<span style="mso-spacerun:
yes"> </span></span><span style='font-size:167%;color:#E9EB5D;
mso-color-index:3'>F1 data = 16.723 = 2^16.723 = 108,174</span></span></layer></div>
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style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index:
3'>These values can all </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index:
3'>be changed by the </span></span></layer><script> - mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.35 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span
style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index:
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<td align=left colspan=1><font face=Helvetica size=3>This slide shows you
the lower parts of the Trait Data and Analysis Form with the data for the
first set of BXD strains</font><br>
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\ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0026.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0026.htm deleted file mode 100755 index 7dac49e1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0026.htm +++ /dev/null @@ -1,130 +0,0 @@ -<html>
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<div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans";
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display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Critiquing 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'> data the Trait Data</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:150%;
color:#E9EB5D;mso-color-index:3'>Use the BASIC STATISTICS button to evaluate
the App data. You will find that App data </span></span></layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * 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:150%;
color:#E9EB5D;mso-color-index:3'>from the different strains are not equally
trustworthy. BXD8 is an obvious outlier without </span></span></layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.04 * 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-family:"Gill Sans";font-size:150%;
color:#E9EB5D;mso-color-index:3'>replication (no error bar)</span><span
style='font-size:150%;color:#E9EB5D;mso-color-index:3'>. BXD33 is also
suspiciously low. BXD5 is noisy. </span><span style='font-family:"Gill Sans";
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display:none'><br>
</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>The Basic Statistics
page allows you to evaluate some aspects of the data quality. In this case,
BXD8 is a potential problem. An outlier of this type may be generated by a
technical artifact (bad sample?). However, it is also possible that BXD8
just has genuine low endogenous expression of App and may therefore be a
particularly valuable model for research. There are different ways to treat
problematic data of these types. One way is simply to discard this datum.
The other way is to prevent outliers from have too much influence
quantitatively, while leaving them in their low (or high positions). This is
called windsorizing the data (after King Henry the VIII who had a habit of
chopping heads). In this case, we have windsorized the BXD8 to a value of 16.0
and the BXD33 to a value of 16.02. Rank is retained. We are making a bet
that the two lowest strains are really low, but we are hedging our bet and
just making them a little lower than BXD90. This removes their ÒundueÓ
influence.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>1. It turns out that
BXD8 is a strain with many odd phenotypes. The whole strain is essentially
an outlier for many traits. Therefore, the low App expression data may be
quite accurate. Still, it would be comforting to have at least two more
replicates.</font><br>
</td>
</tr>
</table>
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display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</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'> expression after
windsorizing</span></div>
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<tr>
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<td align=left colspan=1><font face=Helvetica size=3>Now we get a much
better feel for the variation in the error among the cases. Those without
error bars are of course the ÒnoisiestÓ of all. This data set is not
complete yet (the aim is to acquire at least one male-female sample for each
BXD strain).</font><br>
</td>
</tr>
</table>
</div>
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display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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expression patterns</span></div>
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-
<layer>
<div id=NotesObj style='display:none'>
<table style='color:white' border=0 width="100%">
<tr>
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<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 this
particular App transcript steady-state abundance level correlate with those
of any other transcripts in the same INIA Brain mRNA M430 data set?</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>You can CHOOSE many other DATABASES at this point if
you want, but for now letÕs stick with the default.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. There are different
ways to sort the correlations. The most obvious is by p-value (most
significant values at the top of the list), but it is also interesting to
sort the top 100 or top 500 by their gene symbol (gene ID) or by their
chromosomal location (position).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. If you donÕt want
your analysis to be sensitive to outliers, then you may want to choose to
use the Spearman Rank Order method of calculating correlations.</font><br>
</td>
</tr>
</table>
</div>
</layer>
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display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span
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<tr>
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<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>The Traits Correlation
output window (Correlation Results) compares App expression data with all
other traits in this INIA Brain data set. The most significant 100 or 500
transcripts are sorted by their p-values. The top correlation is that of the
probe set to itself (often a value of 1.0, but in this case we modified the
App values manually by windsorizing the data). The next best correlation is
to another App probe set. The fourth correlation is interesting and suggests
that there may be a link between App and a particular type of ataxia
(Atcay).</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>Use the checkboxes to the far left to select traits
that you want to study together. Once you have selected interesting traits,
click on the ADD SELECTION button. This puts all of the selected traits into
a SELECTIONS WINDOW for other types of analysis.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. The p-value is not
corrected for multiple tests. A conservative approach for array data would
be to assume 10,000 nominally independent tests. Subtract 4 from the
exponent and if the value is still smaller than 0.05 you may have a real
correlation.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. The LITERATURE
CORRELATION is a data type generated by Drs. Ramin Homayouni and Michael
Berry. Click on the header column by the asterisk for more information on
this highly useful data type.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>4. We are using Pearson
product moment correlations rather that the Spearman rank order correlation.
But you can select either in the previous step.</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
-</script><script language=JavaScript><!--
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</body>
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<div style='mso-special-format:nobullet;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%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
348;mso-text-indent-alt:56;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
348;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'><i>App</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> and </span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>Atcay</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript scatterplot </span></div>
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-
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</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>By clicking on the
CORRELATION of the Atcay transcript to the App transcript, you can generate
a Correlation plot between these two transcripts. In this App and Atcay
scatterplot, each point is a strain mean value. For example, BXD33 and BXD8
have low App and Atcay expressions. The two parental strains and the F1 are
also included in this plot.</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/html/webqtl_demo2_part1.ppt_files/slide0031.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0031.htm deleted file mode 100755 index 9a54b689..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0031.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html>
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<div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans";
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348;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'><i>App</i></span><span
style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript and eight of
its neighbors</span></div>
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-</script></div>
</layer></div>
</LAYER>
-
<layer>
<div id=NotesObj style='display:none'>
<table style='color:white' border=0 width="100%">
<tr>
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<td width="100%"></td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>A group of traits from
many different databases can be selected and brought together for joint
analysis. In this case all of the content of the BXD SELECTIONS is from a
single BRAIN database, the top 20 neighbors of the App transcript from the
Correlation Results table. Eight of these neighbors plus App is shown in the
slide.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>All of items in the BXD SELECTIONS were selected using
the SELECT ALL button</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. The buttons at the
top (and bottom) of this page can do some cool stuff. We will work with
NETWORK GRAPH first.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. Think of the
SELECTIONS as your shopping cart. You go to different aisles in the
supermarket to acquire different types of items of interest. These could
include transcripts, classical phenotypes (longevity, brain weight, prepulse
inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves
doing some analysis with the items in the cart.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>4. Different tools
handle different numbers of items. Most will handle up to 100 traits.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><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/html/webqtl_demo2_part1.ppt_files/slide0032.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0032.htm deleted file mode 100755 index 85ee47fe..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0032.htm +++ /dev/null @@ -1,118 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
<link title="Presentation File" type="application/powerpoint" rel=alternate
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<div></div>
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mso-text-raise:0%'><span style='font-size:82%'><i>App</i></span><span
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style='mso-special-format:lastCR;display:none'><br>
</span></div>
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</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>Output of the Network
Graph. Warm colors (orange and red) are positive correlations above 0.5
whereas cool colors (green and blue) are negative correlations. Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3> All of the nodes (gene/transcripts) on this graph are
clickable.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. For this graph the
App expression values have ÒrevertedÓ to their pre-Windsorized values.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>3. To generate this
graph, we used the default setting:<span style="mso-spacerun: yes">
</span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use
curved lines (aka ÒedgesÓ).</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/html/webqtl_demo2_part1.ppt_files/slide0033.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm deleted file mode 100755 index 042ca4ad..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm +++ /dev/null @@ -1,104 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
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<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
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<div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans";
font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none;
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font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
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292;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'>Correlations of </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'> with classical traits</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
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-</script></div>
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<div><script language=JavaScript><!--
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-</script></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>Going back to the Trait
Data and Analysis Form window, we have computed the correlations between
strain variation in App expression level and other classical phenotypes that
have already been measured in many of the same BXD strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Arial size=3>1.</font><font
face=Helvetica size=3>The number of common strains varies widely--in this
case from 14 to 23 strains.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>2. We can add these
traits (four are selected) to our BXD SELECTIONS window.</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/html/webqtl_demo2_part1.ppt_files/slide0034.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0034.htm deleted file mode 100755 index 3cf1ac70..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0034.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html>
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<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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</layer><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.99 * 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 = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:nobullet;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%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
292;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'>Network Graph of </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'> with classical traits</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.08 * g_height; myleft = 0.03 * g_width; myheight = 0.9 * g_height; mywidth = 0.88 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div><script language=JavaScript><!--
-xx = 0.03 * g_width; -yy = 0.08 * g_height; -ht = 0.9 * g_height; -wd = 0.88 * g_width; -document.write( -'<img border=0 src="slide0016_image036.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//-->
-</script></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>We have computed the
Network Graph, now using other types of traits.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Saline Hot Plate
Latency is the green node labeled 10020.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Freezing (fear) is the
green node labeled 10447.</font><br>
</td>
</tr>
<tr>
<td colspan=1></td>
<td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br>
</td>
</tr>
</table>
</div>
</layer>
<script language=JavaScript><!--
-//-->
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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/html/webqtl_demo2_part1.ppt_files/slide0035.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0035.htm deleted file mode 100755 index ca5ac8bb..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0035.htm +++ /dev/null @@ -1,151 +0,0 @@ -<html>
<head>
<meta name=ProgId content=PowerPoint.Slide>
<meta name=Generator content="Microsoft Macintosh PowerPoint 11">
<title>PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics</title>
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href="webqtl_demo2_part1.ppt.ppt">
<script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script>
<meta name=Description content=Aug-15-05>
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-function DoOnLoad() { - LoadNavSld("slide0035.htm"); -}//-->
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bgcolor="#000000">
<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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-ht = g_height; -wd = g_width; -document.write( -'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' ); -//-->
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</layer><script> - mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * 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 = 0.91 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:nobullet;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%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt:
292;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'>Summary of Part 1:</span><span
style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;
display:none'><br>
</span></div>
</layer></div>
</layer><script> - mytop = 0.1 * g_height; myleft = 0.08 * g_width; myheight = 0.47 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div>
<layer>
<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%'></div>
</layer>
<layer>
<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%'></div>
</layer>
<layer>
<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%'></div>
</layer>
<layer>
<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%'></div>
</layer>
<script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.84%;font-family:Arial'>1.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You have learned the basics
about searching for traits<br>
</span></span></layer></div>
</layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.85 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-3.03%;font-family:Arial'>2.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know some methods to check
data quality<br>
</span></span></layer></div>
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<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-3.03%;font-family:Arial'>3.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to edit bad or
suspicious data<br>
</span></span></layer></div>
</layer><script> - mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.85%;font-family:Arial'>4.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to review the
basic statistics of a trait<br>
</span></span></layer></div>
</layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:numbullet;font-family:Arial;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-margin-left-alt:
144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * 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:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.74%;font-family:Arial'>5.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to generate a
scattergram between two </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * 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:200%;
color:#E9EB5D;mso-color-index:3'>traits using the Traits Correlation tool<br>
</span></span></layer></div>
</layer><script> - mytop = 0.31 * 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>
<div style='mso-special-format:numbullet;font-family:Arial;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;
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color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
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style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to add items to
your SELECTIONS window<br>
</span></span></layer></div>
</layer><script> - mytop = 0.37 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script>
<div style='mso-special-format:numbullet;font-family:Arial;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;
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet;
position:absolute;left:-2.57%;font-family:Arial'>7.</span></span><span
style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:
3'><span style="mso-spacerun: yes"> </span>You know how to generate a
Network Graph of traits that </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * 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:200%;
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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:200%;
color:#E9EB5D;mso-color-index:3'>What does genetic covariance mean? The genetic
covariance can </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * 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:200%;
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style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%;
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sampling error or poor </span></span></layer><script> - mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.92 * 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:200%;
color:#E9EB5D;mso-color-index:3'>experimental design. Evaluate the biological
plausibility of </span></span></layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * 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-family:"Gill Sans";font-size:200%;
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genomics</title>
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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;
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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>
</layer></div>
</layer><script> - mytop = 0.16 * g_height; myleft = 0.06 * g_width; myheight = 0.24 * g_height; mywidth = 0.9 * 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 = 0.24 * g_height; mywidth = 0.87 * 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:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * 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:82%'>rwilliam@nb.utmem.edu<br>
</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
style='text-align:left'><span style='font-size:82%'><br>
</span></span></layer><script> - mytop = 0.16 * 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
style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR;
display:none'><br>
</span></span></layer></div>
</layer></div>
</layer><script> - mytop = 0.27 * g_height; myleft = 0.09 * g_width; myheight = 0.07 * g_height; mywidth = 0.5 * 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:
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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:300%;
color:#E9EB5D'>kmanly@utmem.edu</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-family:"Gill Sans";font-size:200%;
color:#E9EB5D'>The </span><span style='font-family:"Gill Sans";font-size:200%;
color:#E9EB5D'><i>App</i></span><span style='font-family:"Gill Sans";
font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part
of an </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:200%;
color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and R. Clark (July
15, </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * 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:200%;
color:#E9EB5D'>2005)</span><span style='font-family:"Gill Sans";font-size:300%;
color:#E9EB5D;mso-special-format:lastCR;display:none'><br>
</span></span></layer></div>
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<td align=left colspan=1><font face=Verdana size=3>END</font><br>
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