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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/tutorial/ppt
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
Diffstat (limited to 'web/tutorial/ppt')
-rwxr-xr-xweb/tutorial/ppt/WebQTLDemo.htm4
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-rwxr-xr-xweb/tutorial/ppt/WebQTLDemo_files/slide0004.htm25
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-rwxr-xr-xweb/tutorial/ppt/WebQTLDemo_files/slide0005.htm25
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-rwxr-xr-xweb/tutorial/ppt/WebQTLDemo_files/slide0006.htm25
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002_notes_pane.htm5
-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003.htm25
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image054.pngbin0 -> 237 bytes
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_image061.pngbin0 -> 1659 bytes
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003_notes_pane.htm5
-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004.htm25
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_notes_pane.htm5
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image019.pngbin0 -> 14905 bytes
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_image039.pngbin0 -> 890 bytes
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_image060.pngbin0 -> 168 bytes
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019_notes_pane.htm5
-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020.htm113
-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image090.pngbin0 -> 237 bytes
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_notes_pane.htm5
-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm110
-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image099.pngbin0 -> 89425 bytes
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm134
-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image102.pngbin0 -> 167566 bytes
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-rwxr-xr-xweb/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023.htm115
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/frame.htm b/web/tutorial/ppt/WebQTLDemo_files/frame.htm
new file mode 100755
index 00000000..ae0e8573
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/frame.htm
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+<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"> <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><script language=JavaScript><!--
+base = parent;//-->
+</script><script language=JavaScript src=script.js></script> </head> <script> <!--
+function getSlideName() {
+ return parent.GetHrefObj( parent.g_currentSlide ).m_slideHref;
+}
+
+function getNotesName() {
+ return parent.GetHrefObj( parent.g_currentSlide ).m_notesHref;
+}
+
+function restore() {
+ self.location.reload();
+}
+
+function WriteMe() {
+ if ( true )
+ document.write( '<frameset cols=\"20%,*\" id=PPTHorizAdjust >' +
+ '<frame src=\"outline_collapsed.htm\" name=PPTOtl>' );
+ var distribution;
+ if ( parent.includeNotes )
+ distribution = "*,20%";
+ else
+ distribution = "*,0";
+ document.write('<frameset rows=\"' + distribution + '\" id=PPTVertAdjust >' +
+ '<frame src=' + getSlideName() + ' name=PPTSld>' +
+ '<frame src=' + getNotesName() + ' name=PPTNts>' );
+ document.write('</frameset>');
+ if ( true )
+ document.write(' </frameset>' );
+}
+
+if ( parent.msie < 0 ) {
+ self.onresize = restore;
+}
+
+WriteMe();
+//-->
+</script> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/fs_navigation_bar.htm b/web/tutorial/ppt/WebQTLDemo_files/fs_navigation_bar.htm
new file mode 100755
index 00000000..d643df26
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/fs_navigation_bar.htm
@@ -0,0 +1,84 @@
+<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> <title>Navigation Bar</title>
+<script>
+<!--
+function restore() {
+if( navigator.platform != "MacPPC" )
+ self.location.reload();
+}
+ mainWin = parent.base;
+ dad = parent;
+function WriteBody()
+{
+ if( window.name != "PPTNav" ) return;
+
+ document.writeln( '<table border=0 valign=top cellpadding=0 cellspacing=0 height=100% width=100%> <tr> <td align=center valign=top> <table border=0 valign=top cellpadding=0 cellspacing=0 height=100%><tr><td align=right valign=top>' );
+ if ( dad.g_hideNav != 1 ) {
+ innerText = "";
+ if ( mainWin.GetHrefObj( mainWin.g_currentSlide ).m_origVisibility == 1 && !mainWin.g_allHidden)
+ innerText = "Slide " + mainWin.GetCurrentSlideNum() + " of " + mainWin.GetNumSlides();
+ else
+ innerText = "Hidden Slide";
+ if( dad.gIsEndShow )
+ innerText = "End of Slide Show";
+
+fEnable = dad.M_HasPrevSld();
+ if( false || fEnable )
+ {
+ prevBtn = "prev_active.gif";
+ document.write( '<a onclick="if(event) event.cancelBubble=true" href="javascript:dad.M_GoPrevSld()" >' );
+ }
+ else
+ prevBtn = "prev_disabled.gif";
+
+ document.write( '<img src="' + prevBtn + '" border=0 alt="Previous Slide" title="Previous Slide">' );
+
+var textAlign;
+ if ( false )
+ textAlign = 'top';
+ else
+ textAlign = 'center';
+
+ if( false || fEnable )
+ document.write( '</a>' );
+
+ document.write( '</td><td align=center valign=' + textAlign + '> &nbsp &nbsp <font face=\"Arial\" color=#000000 size=2>' + innerText + '</font> &nbsp &nbsp </td><td align=left valign=top>' );
+
+
+fEnable = (!dad.gIsEndShow && mainWin.EndSlideShow) || (!mainWin.EndSlideShow &&( mainWin.GetCurrentSlideNum() != mainWin.GetNumSlides() ) );
+ if( false || fEnable )
+ {
+ nextBtn = "next_active.gif";
+ document.write( '<a onclick="if(event) event.cancelBubble=true" href="javascript:dad.M_GoNextSld()" >' );
+ }
+ else
+ nextBtn = "next_disabled.gif";
+ document.write( '<img src="' + nextBtn + '" border=0 alt="Next Slide" title="Next Slide">' );
+
+ if( false || fEnable )
+ document.write( '</a>' );
+ document.write( '</td> </tr></table> </td> <td align=right valign=top>' );
+ document.write( '<a onclick="if(event) event.cancelBubble=true" href="javascript:mainWin.CloseFullScreen()" > ' );
+ document.write( '<img src="fullscrClose.gif"border=0 alt="Close" title="Close">');
+ document.write( ' </a>' );
+ }
+ document.write( '</td> </tr></table>' );
+}
+if ( mainWin.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.onmousedown = handleClick;
+}
+
+function handleClick(event) {
+ if ( event.which == 3 )
+ return false;
+ return true;
+}
+//-->
+</script>
+ </head> <body background=navbg.gif topmargin=2 onresize="restore()" scroll="no" onkeypress="parent.processNavKPH(event)" onclick="parent.processNavClick()"oncontextmenu="parent.processNavClick(); return false"> <center><script language=JavaScript><!--
+WriteBody();//-->
+</script></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/fullscr.gif b/web/tutorial/ppt/WebQTLDemo_files/fullscr.gif
new file mode 100755
index 00000000..85842700
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/fullscr.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/fullscrClose.gif b/web/tutorial/ppt/WebQTLDemo_files/fullscrClose.gif
new file mode 100755
index 00000000..ccd0de13
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/fullscrClose.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/fullscreen.htm b/web/tutorial/ppt/WebQTLDemo_files/fullscreen.htm
new file mode 100755
index 00000000..17916572
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/fullscreen.htm
@@ -0,0 +1,48 @@
+<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 ( ! opener.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script><script language=JavaScript src=script.js></script><script language=JavaScript><!--
+var SCREEN_MODE = "FullScreen";
+ base = self;
+ g_fullscrMode = 1;LoadHTMLVersion();
+//-->
+</script> </head> <script> <!--
+closing = false;
+PPTPRESENTATION = 1;
+function getSlideName() {
+ return opener.GetHrefObj( g_currentSlide ).m_slideHref;
+}
+function initpopup() {
+ if ( base.msie < 0 )
+ NavPopup = window.open( "fs_navigation_bar.htm", "controls", "alwaysRaised=yes,WIDTH=300,HEIGHT=50");
+ else
+ NavPopup = window.open( "fs_navigation_bar.htm", "controls", "WIDTH=300,HEIGHT=50");
+ NavPopup.focus();
+}
+
+
+function WriteMe() {
+ document.write( '<frameset rows=\" *,35 \" frameborder=0> ' +
+ ' ' +
+ '<frame src=\"' + getSlideName() + '\" name=PPTSld marginheight=0 marginwidth=0 scrolling=no noresize> ' +
+ ' <frame src="fs_navigation_bar.htm" name=PPTNav marginheight=0 marginwidth=0 scrolling=no noresize> ' +
+ '</frameset>' );
+ window.focus();
+}
+
+function shutdown( ) {
+if ( ! closing )
+
+ if ( window.NavPopup && !window.NavPopup.closed )
+ window.NavPopup.close();
+}
+
+WriteMe();
+// initpopup();
+
+
+ self.onunload = shutdown;
+
+//-->
+</script> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/master02.htm b/web/tutorial/ppt/WebQTLDemo_files/master02.htm
new file mode 100755
index 00000000..0de623de
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/master02.htm
@@ -0,0 +1,11 @@
+<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"> <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> <link rel=Stylesheet href="master03_stylesheet.css"> <script language=JavaScript src=script.js></script>
+<script>
+<!--
+ parent.location.href=document.all.item("Main-File").href
+//-->
+</script>
+ </head> <body> <div class=O style='text-align:right;position:absolute;top:.53%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black'><b>Memphis Microarray 2003</b></span></div> <div class=O style='position:absolute;top:97.52%;left:1.32%;width:42.78%; height:2.12%'><span style='color:black'><b>June 11, 2003, Rob Williams</b></span></div> <div class=O style='text-align:right;position:absolute;top:97.52%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black;mso-field-code:meta16'><b>Ü#Ý</b></span><span style='color:black;mso-special-format:lastCR'><b><br> </b></span></div> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/master03.htm b/web/tutorial/ppt/WebQTLDemo_files/master03.htm
new file mode 100755
index 00000000..03d92548
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/master03.htm
@@ -0,0 +1,11 @@
+<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"> <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> <link rel=Stylesheet href="master03_stylesheet.css"> <script language=JavaScript src=script.js></script>
+<script>
+<!--
+ parent.location.href=document.all.item("Main-File").href
+//-->
+</script>
+ </head> <body> <div style='position:absolute;top:.35%;left:6.09%;width:90.33%;height:18.55%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/master03_background.gif b/web/tutorial/ppt/WebQTLDemo_files/master03_background.gif
new file mode 100755
index 00000000..271a75e9
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/master03_background.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/master03_stylesheet.css b/web/tutorial/ppt/WebQTLDemo_files/master03_stylesheet.css
new file mode 100755
index 00000000..97cb9745
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+ document.write( '<a href=\"javascript:parent.TP_GoToNextSld()\">' );
+ }
+ else
+ nextBtn = "next_disabled.gif";
+
+document.write( '<img src="' + nextBtn + '" border=0 title="Next Slide" alt="Next Slide">' );
+
+ if( fEnable )
+ document.write( '</a>' );
+ if ( drawing_app ) {
+ document.write( ' &nbsp &nbsp &nbsp &nbsp<a href=\"javascript:parent.GoToLast()\">' );
+ document.write( '<img src="next_active.gif"></a>' );
+ }
+
+
+ document.write( '</td> </tr></table>' );
+
+ if ( ! drawing_app && !false ) {
+ document.write( '</td> <td align=right valign=top>' );
+ document.write( '<a href=\"javascript:parent.FullScreen()\"> ' +
+ '<img src="fullscr.gif" border=0 title="Full Screen Slide Show" alt="Full Screen Slide Show">' +
+ '</a>' );
+ }
+ document.write( '</td> </tr></table>' );
+}
+//-->
+</script>
+ </head> <body background=navbg.gif topmargin=2 scroll="no" onresize="restore()"> <center><script language=JavaScript><!--
+WriteBody();//-->
+</script></center> </body> </html> \ No newline at end of file
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index 00000000..d680812c
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/outline_collapsed.htm
@@ -0,0 +1,5 @@
+<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 >&gt;</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 width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >&gt;</ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>&quot;or webqtl.org/search.html...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF>&quot;First page of data:&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>&quot;Data sources:&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>&quot;Return to Trait Data page&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>&quot;Discovering shared expression patterns&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>&quot;The App transcript neighborhood&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>&quot;Handdrawn sketch of the neighborhood&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>&quot;What a network is likely...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>&quot;2.45 billion scatter plots&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>&quot;Cross-tissue type correlations&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>&quot;Cross-modal correlations:&quot;</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 >&gt;</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">&nbsp;&nbsp;&nbsp; </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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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">&nbsp;&nbsp;&nbsp; </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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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
new file mode 100755
index 00000000..c8c72b13
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/outline_expand.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm b/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm
new file mode 100755
index 00000000..3e6bdf31
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/outline_expanded.htm
@@ -0,0 +1,5 @@
+<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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>&quot;or webqtl.org/search.html...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF>&quot;First page of data:&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>&quot;Data sources:&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>&quot;Return to Trait Data page&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>&quot;Discovering shared expression patterns&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>&quot;The App transcript neighborhood&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>&quot;Handdrawn sketch of the neighborhood&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>&quot;What a network is likely...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>&quot;2.45 billion scatter plots&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>&quot;Cross-tissue type correlations&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>&quot;Cross-modal correlations:&quot;</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 >&gt;</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">&nbsp;&nbsp;&nbsp; </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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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">&nbsp;&nbsp;&nbsp; </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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</ilayer>'); 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+ }
+ 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=32, 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),
+ new hrefList("slide0019.htm", 1, 19),
+ new hrefList("slide0020.htm", 1, 20),
+ new hrefList("slide0021.htm", 1, 21),
+ new hrefList("slide0022.htm", 1, 22),
+ new hrefList("slide0023.htm", 1, 23),
+ new hrefList("slide0024.htm", 1, 24),
+ new hrefList("slide0025.htm", 1, 25),
+ new hrefList("slide0026.htm", 1, 26),
+ new hrefList("slide0027.htm", 1, 27),
+ new hrefList("slide0028.htm", 1, 28),
+ new hrefList("slide0029.htm", 1, 29),
+ new hrefList("slide0030.htm", 1, 30),
+ new hrefList("slide0031.htm", 1, 31),
+ 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( " > &nbsp " + 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 );
+ ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF );
+ }
+}
+
+function hrefList( slideHref, notesHref, visible, slideIdx, type )
+{
+ this.m_slideHref = slideHref;
+ this.m_notesHref = notesHref;
+ this.m_navbarHref = NAVBAR_HREF;
+ this.m_origVisibility = visible;
+ this.m_visibility = visible;
+ this.m_slideIdx = slideIdx;
+ this.type = type;
+}
+
+function IsFullScrMode() {
+ return g_fullscrMode;
+}
+
+
+function IsFramesMode() {
+ return (1 - g_fullscrMode);
+}
+
+function SldUpdated( id )
+{
+ if ( ( id != GetHrefObj( g_currentSlide ).m_slideHref ) || ( g_currentSlide == g_lastVisibleSld ) ){
+ g_prevSlide = g_currentSlide;
+ g_currentSlide = GetSlideNum( id );
+ obj = GetHrefObj( g_currentSlide );
+ if( !SIMPLE_FRAMESET )
+ ChangeFrame( NOTES_FRAME, obj.m_notesHref );
+ ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF );
+ }
+}
+
+function ToggleOutline() {
+ g_showoutline = 1 - g_showoutline;
+ writeMyFrame();
+}
+
+function ShowHideNotes() {
+ g_shownotes = 1 - g_shownotes;
+ writeMyFrame();
+}
+
+function writeMyFrame() {
+ SetFSMode(0);
+ obj = frames[MAIN_FRAME];
+
+ var curslide = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_slideHref;
+ var curnotes = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_notesHref;
+ var otlhref = g_baseURL + "/" + g_outline_href;
+ if ( msie < 0 ) {
+ if ( ! g_showoutline && g_shownotes ) {
+ obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \
+ <frameset rows=\"*,20%\" id=\"frameset2\" > \
+ <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \
+ <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \
+ </frameset> </html>' );
+ }
+ else if( g_showoutline && g_shownotes ){
+ obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \
+ <frameset cols=\"20%,*\" id=\"frameset1\"> \
+ <frame src=\"' + otlhref + '\" name=PPTOtl> \
+ <frameset rows=\"*,20%\" id=\"frameset2\" > \
+ <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \
+ <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \
+ </frameset> </frameset></html>' );
+ }
+ else if ( !g_shownotes && !g_showoutline ) {
+ obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \
+ <frameset rows="*,0" frameborder=0 > \
+ <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \
+ </frameset> </html>' );
+ }
+ else if( !g_shownotes && g_showoutline ) {
+ obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \
+ <frameset cols=\"20%,*\" id=\"frameset1\"> \
+ <frame src=\"' + otlhref + '\" name=PPTOtl> \
+ <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \
+ </frameset></html>' );
+ }
+ obj.document.close();
+ }
+ else {
+ if ( g_showoutline ) {
+ obj.PPTHorizAdjust.cols = "20%,*";
+ obj.PPTOtl.location.reload();
+ }
+ else {
+ obj.PPTHorizAdjust.cols = "0,*";
+ }
+ if ( g_shownotes ) {
+ obj.PPTVertAdjust.rows = "*,20%";
+ obj.PPTNts.location.href = curnotes;
+ }
+ else {
+ obj.PPTVertAdjust.rows = "*,0";
+ }
+ }
+ ChangeFrame( OUTLINE_NAVBAR_FRAME, OUTLINE_NAVBAR_HREF );
+}
+
+function FullScreen() {
+ g_done = 0;
+
+
+ SetFSMode(1);
+ if ( msie >= 0 )
+ FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", null, "fullscreen=yes");
+ else {
+ var height = screen.availHeight;
+ if ( window.navigator.platform.indexOf( "Mac" ) >= 0 ) {
+ height -= 30;
+ }
+ FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", "null", "height="+ height + ",width=" + screen.availWidth + ",screenX=0,screenY=0");
+ }
+}
+
+function SetFSMode( i ) {
+
+}
+
+function Slide( i ) {
+ SetFSMode(0);
+ GoToSld(GetHrefObj(i).m_slideHref);
+}
+
+function TP_GoToNextSld() {
+ SetFSMode(0);
+ GoToNextSld();
+}
+
+function TP_GoToPrevSld() {
+ SetFSMode(0);
+ GoToPrevSld();
+}
+
+function CloseFullScreen() {
+ g_done = 0;
+
+ if ( IsNav() ){
+ if ( self.opener )
+ opener.FSWin = null;
+ }
+ window.close();
+}
+
+function slidenum(i) {
+ var slidename = "slide";
+ if ( i < 10 )
+ return ( slidename + "000" + i);
+ else if ( i < 100 )
+ return ( slidename + "00" + i );
+ else if ( i < 1000 )
+ return (slidename + "0" + i );
+ else
+ return (slidename + i );
+}
+function UpdateLastVisibleSlide( index ) {
+ if ( g_lastVisibleSld < index )
+ g_lastVisibleSld = index;
+}
+
+function jpegArray( numSlides ) {
+count_hidden = 0;
+ g_docTable = new Array();
+ for( i=0; i<numSlides; i++ ) {
+ j = 2 * 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, "jpeg" );
+ else
+ g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "jpeg" );
+ if ( !g_hiddenSlide[i] ) count_hidden++;
+ else UpdateLastVisibleSlide( i+1 );
+ }
+}
+
+function ieArray( numSlides ) {
+count_hidden = 0;
+ g_docTable = new Array();
+ for( i=0; i<numSlides; i++ ) {
+ var str = slidenum(i+1) +".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, "ie" );
+ 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( 32 );
+ 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( 32 );
+ }
+ else
+ window.location.replace( "WebQTLDemo_files/error.htm" );
+ }
+ else {
+ if ( isNAVFiles > 0 && ver < 5)
+ navArray( 32 );
+ 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( 32 );
+ }
+ else
+ window.location.replace( "WebQTLDemo_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( "WebQTLDemo_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 ( 32 );
+ }
+
+}
+
+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/WebQTLDemo_files/slide0001.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0001.htm
new file mode 100755
index 00000000..4c783452
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0001.htm
@@ -0,0 +1,25 @@
+<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: WebQTL Demonstration One please link to www.webqtl.org/search.html"> <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="slide0001.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: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 &#1;";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 &#1;";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">&nbsp;&nbsp; </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
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new file mode 100755
index 00000000..5bcd338f
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Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm
new file mode 100755
index 00000000..0df634c1
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0001_notes_pane.htm
@@ -0,0 +1,5 @@
+<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">&nbsp;&nbsp; </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
new file mode 100755
index 00000000..2efd97f9
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0002.htm
@@ -0,0 +1,25 @@
+<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="slide0002.htm"
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+ 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: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">&nbsp; </span>To get to a version of the window shown above you will need to click on the phrase<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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
new file mode 100755
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Binary files differ
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new file mode 100755
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Binary files differ
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Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm
new file mode 100755
index 00000000..266bf3fb
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0002_notes_pane.htm
@@ -0,0 +1,5 @@
+<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">&nbsp; </span>To get to a version of the window shown above you will need to click on the phrase<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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
new file mode 100755
index 00000000..7e0f4be9
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0003.htm
@@ -0,0 +1,25 @@
+<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;} --> </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
new file mode 100755
index 00000000..5c7d29e8
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image005.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif
new file mode 100755
index 00000000..f75379b9
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0003_image006.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm
new file mode 100755
index 00000000..5dbbbd2e
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0003_notes_pane.htm
@@ -0,0 +1,5 @@
+<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
new file mode 100755
index 00000000..9980cf8b
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0004.htm
@@ -0,0 +1,25 @@
+<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> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004_image007.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0004_image007.gif
new file mode 100755
index 00000000..db14d732
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0004_image007.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004_image008.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0004_image008.gif
new file mode 100755
index 00000000..8ac35a66
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0004_image008.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0004_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0004_notes_pane.htm
new file mode 100755
index 00000000..22def119
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0004_notes_pane.htm
@@ -0,0 +1,5 @@
+<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 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
new file mode 100755
index 00000000..ab904a72
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0005.htm
@@ -0,0 +1,25 @@
+<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">&nbsp; </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
new file mode 100755
index 00000000..a6596e12
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0005_image009.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm
new file mode 100755
index 00000000..916084ec
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0005_notes_pane.htm
@@ -0,0 +1,5 @@
+<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">&nbsp; </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
new file mode 100755
index 00000000..f3d4d1d5
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0006.htm
@@ -0,0 +1,25 @@
+<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">&nbsp;&nbsp; </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">&nbsp; </span>slide shows you the<span style="mso-spacerun: yes">&nbsp; </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
new file mode 100755
index 00000000..967e59ca
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image010.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif
new file mode 100755
index 00000000..1e1432cf
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0006_image011.gif
Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm
new file mode 100755
index 00000000..be43575c
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0006_notes_pane.htm
@@ -0,0 +1,5 @@
+<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">&nbsp; </span>slide shows you the<span style="mso-spacerun: yes">&nbsp; </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
new file mode 100755
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+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
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm
new file mode 100755
index 00000000..7d2536da
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0007_notes_pane.htm
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+<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
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+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>&gt;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">&nbsp; </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
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new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm
new file mode 100755
index 00000000..5003f4a6
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0008_notes_pane.htm
@@ -0,0 +1,5 @@
+<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">&nbsp; </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
new file mode 100755
index 00000000..82b93d4f
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+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0009.htm
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+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="slide0009.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: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">&nbsp; </span>These are Pearson product moment correlations and they are sensitive to outliers. If you prefer, you can recompute Spearman rank order correlations.</font><br> </td> </tr> <tr> <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">&nbsp; </span>conventions in this correlation network sketch.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=3>1.</font><font face=Helvetica size=3>The official gene symbol = App</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. OUr estimate of the location of these gene in the Mouse Genome Sequencing Consoritum version 3 build (MGSCv3). Chromosome followed by the megabase position relative to the centromere. (Mice only have one chromosome arm so this is an unambiguous coordinate. )</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. The pair of numbers: top is the highest expression among the strain set. The lower number is the lowest expression of that transcript among the strain set.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. Vertical number on the right side of each box: this is the probe set ID given by Affymetrix. We have truncated these probe set IDs so you will not see the usual<span style="mso-spacerun: yes">&nbsp; </span>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">&nbsp; </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
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm
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index 00000000..bdcc6cd9
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0009_notes_pane.htm
@@ -0,0 +1,5 @@
+<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>Many of the data types in the previous slide are hot-linked and it is easy to generate a small web of correlations between any transcript of interest and many other transcripts. In this case, we have used green lines between transcripts that have positive correlations, and red lines between transcripts that have negative correlations. Correlations have been multiplied by 100. The correlation of 0.96 between App and Hsp84-1 reads 96.<span style="mso-spacerun: yes">&nbsp; </span>These are Pearson product moment correlations and they are sensitive to outliers. If you prefer, you can recompute Spearman rank order correlations.</font><br> </td> </tr> <tr> <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">&nbsp; </span>conventions in this correlation network sketch.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=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">&nbsp; </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">&nbsp; </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
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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: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">&nbsp; </span>(www.lumeta.com). It actually illustrates the structure of connections across the<span style="mso-spacerun: yes">&nbsp; </span>Internet. The large green area is a major Internet provider (WorldCom before the fall?).<span style="mso-spacerun: yes">&nbsp; </span>Check<span style="mso-spacerun: yes">&nbsp; </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> <script language=JavaScript><!--
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+<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 ) {
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+</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>What networks are likely to really look like. This slide is taken from Lumeta Inc.<span style="mso-spacerun: yes">&nbsp; </span>(www.lumeta.com). It actually illustrates the structure of connections across the<span style="mso-spacerun: yes">&nbsp; </span>Internet. The large green area is a major Internet provider (WorldCom before the fall?).<span style="mso-spacerun: yes">&nbsp; </span>Check<span style="mso-spacerun: yes">&nbsp; </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> </body> </html> \ No newline at end of file
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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:3.53%;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 &#1;";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">&nbsp; </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() {
+
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+//-->
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new file mode 100755
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+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0011_notes_pane.htm
@@ -0,0 +1,5 @@
+<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>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">&nbsp; </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> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0012.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0012.htm
new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
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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: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">&nbsp; </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">&nbsp; </span>correlations come for a common reference population, none<span style="mso-spacerun: yes">&nbsp; </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> <script language=JavaScript><!--
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+<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 correlation between App and heat shock protein 84-1 transcript is most impressive.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </span>correlations come for a common reference population, none<span style="mso-spacerun: yes">&nbsp; </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
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+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><!--
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+</script><script for=window event=onload language=JavaScript><!--
+if( !IsSldOrNts() ) return;
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+LoadSld( gId );
+playList();MakeSldVis(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.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> </tr> </table> </div> <script language=JavaScript><!--
+function playList() {
+
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+//-->
+</script> </body> </html> \ No newline at end of file
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+<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>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> \ No newline at end of file
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+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="slide0014.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><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() {
+
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+//-->
+</script> </body> </html> \ No newline at end of file
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+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0014_notes_pane.htm
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+<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>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> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0015.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0015.htm
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+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> <!--.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="slide0015.htm"
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+}
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+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: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 &#1;";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">&nbsp;&nbsp;&nbsp; </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 &#1;";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><!--
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+<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 ) {
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+</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
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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:"&#1; 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:"&#1; 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:"&#1;%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:"&#1;%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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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">&nbsp; </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">&nbsp; </span>out during inbreeding. For example, there is no extant BXD3 or BXD4 strain.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!--
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+<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" );
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+</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 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">&nbsp; </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">&nbsp; </span>out during inbreeding. For example, there is no extant BXD3 or BXD4 strain.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file
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+</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><!--
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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%'><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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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'>&gt;&gt;&gt;&gt;PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR &gt;&gt;&gt;&gt;&gt;</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>&#4;<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>&#4;<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>&#4;<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>&#4;<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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun: yes">&nbsp; </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><!--
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+</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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun: yes">&nbsp; </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
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+</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">&nbsp; </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">&nbsp; </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
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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: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 &#1;";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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </span>peaks at a value<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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><!--
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+if ( ! top.PPTPRESENTATION ) {
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+</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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </span>peaks at a value<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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> \ No newline at end of file
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+</script> <meta name=Description content="Jun-19-03: The whole neighborhood is modulated!"> <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><!--
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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: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 &#1;";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">&nbsp; </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> <script language=JavaScript><!--
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+</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>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">&nbsp; </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> \ No newline at end of file
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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: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 &#1;";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>&amp;<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">&nbsp;</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">&nbsp; </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><!--
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+<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="Times New Roman" size=4><b>Candidate Genes: </b><span style="mso-spacerun: yes">&nbsp;</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">&nbsp; </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
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+<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="slide0022.htm"
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+}
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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:1.59%;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">&nbsp; </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><!--
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+
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+</script> </body> </html> \ No newline at end of file
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0022_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0022_notes_pane.htm
new file mode 100755
index 00000000..5ab1a7fe
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0022_notes_pane.htm
@@ -0,0 +1,5 @@
+<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>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">&nbsp; </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
new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
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+LoadSld( gId );
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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: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">&nbsp; </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">&nbsp; </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><!--
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+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0023_notes_pane.htm
@@ -0,0 +1,5 @@
+<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>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">&nbsp; </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">&nbsp; </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
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
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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%'><img 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> <script language=JavaScript><!--
+function playList() {
+
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+//-->
+</script> </body> </html> \ No newline at end of file
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+<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" );
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+</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 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> \ No newline at end of file
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Jun-19-03: Is there known biology to link Hars2 with App? "> <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><!--
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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:-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 &#1;";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">&nbsp;</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> <script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0025_image105.gif b/web/tutorial/ppt/WebQTLDemo_files/slide0025_image105.gif
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0025_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0025_notes_pane.htm
new file mode 100755
index 00000000..ef04157c
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0025_notes_pane.htm
@@ -0,0 +1,5 @@
+<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>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> \ No newline at end of file
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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 &#1;";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">&nbsp;&nbsp;&nbsp; </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 &#1;";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">&nbsp; </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">&nbsp; </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() {
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+<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 ) {
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+</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">&nbsp; </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">&nbsp; </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> \ No newline at end of file
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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:2.29%;left:2.51%;width:108.47%;height:18.9%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 &#1;";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 &#1;";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">&nbsp; </span>correlation with D2Mit423 as shown in the slide above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>By clicking on the symbol D2Mit423 in the Correlation window, you will generate a new Trait Data window shown on the next slide.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!--
+function playList() {
+
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+//-->
+</script> </body> </html> \ No newline at end of file
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+<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 ) {
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+}
+</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>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">&nbsp; </span>correlation with D2Mit423 as shown in the slide above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=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> \ No newline at end of file
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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:-1.23%;left:2.51%;width:110.06%;height:11.66%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:" 0 &#1;";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">&nbsp; </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> <script language=JavaScript><!--
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+<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>We can review the set of correlations between the marker D2Mit423 and all transcripts in forebrain.<span style="mso-spacerun: yes">&nbsp; </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> \ No newline at end of file
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+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="slide0029.htm"
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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:-.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 &#1;";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 &#1;";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> <img border=0 src="slide0029_image114.gif" style='position:absolute;top:39.22%; left:48.21%;width:12.18%;height:5.47%'></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 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">&nbsp; </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> </div> <script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
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new file mode 100755
index 00000000..62c56ca6
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+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0029_notes_pane.htm
@@ -0,0 +1,5 @@
+<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>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">&nbsp; </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> \ No newline at end of file
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+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;
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+}
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+</script><script for=window event=onload language=JavaScript><!--
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+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 &#1;";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> \ No newline at end of file
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new file mode 100755
index 00000000..88bd6165
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0030_notes_pane.htm
@@ -0,0 +1,5 @@
+<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>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> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0031.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0031.htm
new file mode 100755
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+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 {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="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 &#1;";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">&nbsp; </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> \ No newline at end of file
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Binary files differ
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0031_notes_pane.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0031_notes_pane.htm
new file mode 100755
index 00000000..435ca8e2
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0031_notes_pane.htm
@@ -0,0 +1,5 @@
+<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>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">&nbsp; </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
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new file mode 100755
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+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> <!--.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="slide0032.htm"
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+ document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref);
+}
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+var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1;
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+
+}
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+document.write(
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+</script> <div><script>
+ mytop = 0 * g_height; myleft = 0.01 * 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 &#1;";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:" 0 &#1;";mso-margin-left-alt:232; mso-text-indent-alt:0'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ 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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width;
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+ mytop = 0.76 * g_height; myleft = 0.04 * g_width; myheight = 0.13 * g_height; mywidth = 0.78 * 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 = 0.77 * 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>PowerPoint ÒNormal viewÓ has notes that </i></span></span></layer><script>
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+</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> </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>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">&nbsp;&nbsp; </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> </layer> <script language=JavaScript><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
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new file mode 100755
index 00000000..343c0d37
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
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+function font_size() {
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+document.onmousedown = _KPH ;
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+function DoOnLoad() {
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+wd = g_width;
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+</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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";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'>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> <div><script language=JavaScript><!--
+xx = 0.02 * g_width;
+yy = 0.16 * g_height;
+ht = 0.81 * g_height;
+wd = 0.71 * g_width;
+document.write(
+'<img border=0 src="slide0002_image002.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.49 * g_height; myleft = 0.42 * g_width; myheight = 0.07 * g_height; mywidth = 0.2 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.42 * g_width;
+yy = 0.49 * g_height;
+ht = 0.07 * g_height;
+wd = 0.2 * g_width;
+document.write(
+'<img border=0 src="slide0002_image003.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.5 * g_height; myleft = 0.62 * g_width; myheight = 0.36 * g_height; mywidth = 0.15 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.62 * g_width;
+yy = 0.5 * g_height;
+ht = 0.36 * g_height;
+wd = 0.15 * g_width;
+document.write(
+'<img border=0 src="slide0002_image004.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.6 * g_height; myleft = 0.79 * g_width; myheight = 0.11 * 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 = 0.05 * g_height; mywidth = 0.15 * 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'>choose a<br> </span></div> </layer><script>
+ mytop = 0.05 * 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-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>database</span></div> </layer></div> </layer><script>
+ mytop = 0.46 * g_height; myleft = 0.79 * g_width; myheight = 0.11 * g_height; mywidth = 0.21 * 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 = 0.18 * 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; 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%; mso-text-raise:0%'><script>
+ mytop = 0 * g_height; myleft = 0 * 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><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>select<br> </span></div> </layer><script>
+ mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.11 * 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'>search</span></div> </layer></div> </layer><script>
+ mytop = 0 * g_height; myleft = 0.03 * g_width; myheight = 0.09 * 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> <layer> <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%; mso-text-raise:0%'></div> </layer> <layer> <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%; mso-text-raise:0%'></div> </layer> <layer> <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%; mso-text-raise:0%'></div> </layer> <layer> <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%; mso-text-raise:0%'></div> </layer> <script>
+ mytop = 0 * g_height; myleft = 0 * 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:" 0 ";mso-margin-left-alt: 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">&nbsp; </span>To get to a version of the window shown above you will need to click on the phrase<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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
new file mode 100755
index 00000000..c53c9bbc
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+function font_size() {
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+ mytop = 0.68 * g_height; myleft = 0.78 * g_width; myheight = 0.17 * g_height; mywidth = 0.21 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ 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> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>highlight<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<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; 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> </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; 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:91%'>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>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><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0036.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0036.htm
new file mode 100755
index 00000000..ae7843aa
--- /dev/null
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <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>
+function font_size() {
+ var min = window.innerWidth/20;
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+document.captureEvents(Event.KEYPRESS);
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+function DoOnLoad() {
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+}//-->
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+ht = g_height;
+wd = g_width;
+document.write(
+'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.14 * g_height; mywidth = 0.97 * 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 = 0.95 * 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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";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'>First page of data: The ÒTrait Data FormÓ</span></div> </layer></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.03 * g_width;
+yy = 0.11 * g_height;
+ht = 0.86 * g_height;
+wd = 0.77 * g_width;
+document.write(
+'<img border=0 src="slide0004_image007.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.56 * g_height; myleft = 0.66 * g_width; myheight = 0.07 * g_height; mywidth = 0.14 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.66 * g_width;
+yy = 0.56 * g_height;
+ht = 0.07 * g_height;
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+document.write(
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+//-->
+</script></div> </layer><script>
+ mytop = 0.5 * g_height; myleft = 0.81 * 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 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 = 0.2 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><span style='font-size:200%;color:#E9EB5D'><i>Click here<br> </i></span></div> </layer><script>
+ mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * 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> </layer><script>
+ mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><span style='font-size:200%;color:#E9EB5D'><i>about<br> </i></span></div> </layer><script>
+ mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><span style='font-size:200%;color:#E9EB5D'><i>data<br> </i></span></div> </layer><script>
+ mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.16 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><span style='font-size:200%;color:#E9EB5D'><i>source</i></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>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><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm
new file mode 100755
index 00000000..bb776db5
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0037.htm
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <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>
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+ self.location.reload();
+}
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+ document.SlideLayer.width = window.innerWidth;
+ document.SlideLayer.height = window.innerHeight;
+}
+document.captureEvents(Event.MOUSEDOWN);
+document.captureEvents(Event.KEYPRESS);
+document.onkeypress = _KPH ;
+document.onmousedown = _KPH ;
+ parent.base.highlite();
+</script><script language=JavaScript><!--
+function DoOnLoad() {
+ LoadNavSld("slide0037.htm");
+}//-->
+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script>
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+ht = g_height;
+wd = g_width;
+document.write(
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+//-->
+</script></div> </layer><script>
+ mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.96 * 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 = 0.94 * 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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";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'>Data sources: Phenotpyes and genotypes</span></div> </layer></div> </layer><script>
+ mytop = 0.1 * g_height; myleft = 0.07 * g_width; myheight = 0.88 * g_height; mywidth = 0.84 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.07 * g_width;
+yy = 0.1 * g_height;
+ht = 0.88 * g_height;
+wd = 0.84 * g_width;
+document.write(
+'<img border=0 src="slide0005_image009.gif" 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>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">&nbsp; </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> </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/slide0038.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0038.htm
new file mode 100755
index 00000000..b3e613ca
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0038.htm
@@ -0,0 +1,119 @@
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <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>
+function font_size() {
+ var min = window.innerWidth/20;
+ if ( min > window.innerHeight/20 )
+ min = window.innerHeight/20;
+
+ return min+"pt";
+}
+var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"];
+function restore() {
+ self.location.reload();
+}
+function set_size() {
+ document.SlideLayer.width = window.innerWidth;
+ document.SlideLayer.height = window.innerHeight;
+}
+document.captureEvents(Event.MOUSEDOWN);
+document.captureEvents(Event.KEYPRESS);
+document.onkeypress = _KPH ;
+document.onmousedown = _KPH ;
+ parent.base.highlite();
+</script><script language=JavaScript><!--
+function DoOnLoad() {
+ LoadNavSld("slide0038.htm");
+}//-->
+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script>
+
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+
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+function new_font_size() {
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+ if ( size < 1 ) size = 1;
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+</script> <div><script language=JavaScript><!--
+ht = g_height;
+wd = g_width;
+document.write(
+'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.47 * 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 = 0.05 * g_height; mywidth = 0.45 * 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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";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:81%;color:#E9EB5D;mso-color-index:3'>Return to Trait Data page </span></div> </layer></div> </layer><script>
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+</script> <div><script language=JavaScript><!--
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+yy = 0.07 * g_height;
+ht = 0.79 * g_height;
+wd = 0.48 * g_width;
+document.write(
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+//-->
+</script></div> </layer><script>
+ mytop = 0.07 * g_height; myleft = 0.5 * g_width; myheight = 0.78 * g_height; mywidth = 0.48 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.5 * g_width;
+yy = 0.07 * g_height;
+ht = 0.78 * g_height;
+wd = 0.48 * g_width;
+document.write(
+'<img border=0 src="slide0006_image011.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.01 * g_height; myleft = 0.52 * g_width; myheight = 0.13 * g_height; mywidth = 0.43 * 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 = 0.05 * g_height; mywidth = 0.4 * 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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";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:81%;color:#E9EB5D;mso-color-index:3'>bottom of this page</span></div> </layer></div> </layer><script>
+ mytop = 0.86 * g_height; myleft = 0.03 * g_width; myheight = 0.11 * g_height; mywidth = 1.09 * 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 = 0.05 * 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">&nbsp;&nbsp; </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> </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>This<span style="mso-spacerun: yes">&nbsp; </span>slide shows you the<span style="mso-spacerun: yes">&nbsp; </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><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm
new file mode 100755
index 00000000..0b96295c
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0039.htm
@@ -0,0 +1,104 @@
+<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> <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> <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>
+function font_size() {
+ var min = window.innerWidth/20;
+ if ( min > window.innerHeight/20 )
+ min = window.innerHeight/20;
+
+ return min+"pt";
+}
+var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"];
+function restore() {
+ self.location.reload();
+}
+function set_size() {
+ document.SlideLayer.width = window.innerWidth;
+ document.SlideLayer.height = window.innerHeight;
+}
+document.captureEvents(Event.MOUSEDOWN);
+document.captureEvents(Event.KEYPRESS);
+document.onkeypress = _KPH ;
+document.onmousedown = _KPH ;
+ parent.base.highlite();
+</script><script language=JavaScript><!--
+function DoOnLoad() {
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+</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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";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'>Discovering shared expression patterns</span></div> </layer></div> </layer><script>
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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>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> </layer> <script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0040.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0040.htm
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+ 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 = 0.9 * 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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";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'>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> </layer></div> </layer><script>
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+</script></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span 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; mso-color-index:3'><b>How </b></span></span></layer><script>
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+</script><span style='text-align:left'><span style='font-size:133%;color:#E9EB5D;mso-color-index: 3'><b>&gt;0.7? What does </b></span></span></layer><script>
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+</script><span style='text-align:left'><span style='font-size:133%;color:#E9EB5D;mso-color-index: 3'><b>this imply.</b></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=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">&nbsp; </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> </layer> <script language=JavaScript><!--
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+</script><script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0041.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0041.htm
new file mode 100755
index 00000000..df4bc799
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+</script> <div><script>
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+ 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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";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'>Handdrawn sketch of the neighborhood</span></div> </layer></div> </layer><script>
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+</script> <div><script language=JavaScript><!--
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+yy = 0.13 * g_height;
+ht = 0.8 * g_height;
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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>Many of the data types in the previous slide are hot-linked and it is easy to generate a small web of correlations between any transcript of interest and many other transcripts. In this case, we have used green lines between transcripts that have positive correlations, and red lines between transcripts that have negative correlations. Correlations have been multiplied by 100. The correlation of 0.96 between App and Hsp84-1 reads 96.<span style="mso-spacerun: yes">&nbsp; </span>These are Pearson product moment correlations and they are sensitive to outliers. If you prefer, you can recompute Spearman rank order correlations.</font><br> </td> </tr> <tr> <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">&nbsp; </span>conventions in this correlation network sketch.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=3>1.</font><font face=Helvetica size=3>The official gene symbol = App</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. OUr estimate of the location of these gene in the Mouse Genome Sequencing Consoritum version 3 build (MGSCv3). Chromosome followed by the megabase position relative to the centromere. (Mice only have one chromosome arm so this is an unambiguous coordinate. )</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. The pair of numbers: top is the highest expression among the strain set. The lower number is the lowest expression of that transcript among the strain set.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. Vertical number on the right side of each box: this is the probe set ID given by Affymetrix. We have truncated these probe set IDs so you will not see the usual<span style="mso-spacerun: yes">&nbsp; </span>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">&nbsp; </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> </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/slide0042.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0042.htm
new file mode 100755
index 00000000..9cc37896
--- /dev/null
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+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.12 * g_height; mywidth = 1.05 * g_width;
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+</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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+//-->
+</script><script language=JavaScript><!--
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+</script> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0043.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0043.htm
new file mode 100755
index 00000000..e0be795e
--- /dev/null
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 &#1;";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:" 0 &#1;";mso-margin-left-alt:232; mso-text-indent-alt:0'><script>
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+</script><span 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>
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+</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>
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+</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> </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>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">&nbsp; </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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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0044.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0044.htm
new file mode 100755
index 00000000..06443316
--- /dev/null
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+</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:" 0 ";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:" 0 ";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'>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> </layer></div> </layer><script>
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+</script> <div><script language=JavaScript><!--
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+//-->
+</script></div> </layer><script>
+ mytop = 0.77 * g_height; myleft = 0.41 * g_width; myheight = 0.07 * 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%'><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> </layer><script>
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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>The correlation between App and heat shock protein 84-1 transcript is most impressive.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </span>correlations come for a common reference population, none<span style="mso-spacerun: yes">&nbsp; </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> </layer> <script language=JavaScript><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
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new file mode 100755
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+</script> <div><script>
+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.9 * 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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";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'>Cross-tissue type correlations</span></div> </layer></div> </layer><script>
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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>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> </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/slide0046.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0046.htm
new file mode 100755
index 00000000..77bd0a8b
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
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+</script> <meta name=Description content=Jun-19-03> <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>
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+}//-->
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+ 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 = 1.05 * 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:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><script>
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+ 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:106%;color:#E9EB5D;mso-color-index:3'>Cross-modal correlations: From mRNA to to </span></span></layer><script>
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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>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> </layer> <script language=JavaScript><!--
+//-->
+</script><script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0047.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0047.htm
new file mode 100755
index 00000000..9f73a171
--- /dev/null
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+//-->
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+function playList() {
+
+}
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0048.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0048.htm
new file mode 100755
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+ 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:"&#1; 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:"&#1; 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="slide0016_image028.gif" 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="slide0016_image029.gif" 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="slide0016_image030.gif" 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="slide0016_image031.gif" 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="slide0016_image032.gif" 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="slide0016_image033.gif" 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:" 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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:"&#1; 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 + ' >' );
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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>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">&nbsp; </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">&nbsp; </span>out during inbreeding. For example, there is no extant BXD3 or BXD4 strain.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!--
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+function playList() {
+
+}
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+function DoOnLoad() {
+ LoadNavSld("slide0049.htm");
+}//-->
+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' 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> <div id=SlideObj class=sld style='position:relative;font-size:&{new_font_size()};'><script>
+ mytop = 0 * g_height; myleft = 0 * g_width; myheight = 1 * g_height; mywidth = 1 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+ht = g_height;
+wd = g_width;
+document.write(
+'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.4 * g_height; myleft = 0.73 * 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><script language=JavaScript><!--
+xx = 0.73 * g_width;
+yy = 0.4 * g_height;
+ht = 0.05 * g_height;
+wd = 0.14 * g_width;
+document.write(
+'<img border=0 src="slide0017_image074.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.4 * g_height; myleft = 0.74 * 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 = 0.04 * g_height; mywidth = 0.11 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='mso-line-spacing:"&#1; 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white'>aa<br> </span></div> </layer><script>
+ mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='mso-line-spacing:"&#1; 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script>
+ mytop = 0.16 * g_height; myleft = 0.73 * 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><script language=JavaScript><!--
+xx = 0.73 * g_width;
+yy = 0.16 * g_height;
+ht = 0.05 * g_height;
+wd = 0.14 * g_width;
+document.write(
+'<img border=0 src="slide0017_image075.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.16 * g_height; myleft = 0.74 * 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 = 0.04 * g_height; mywidth = 0.11 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='mso-line-spacing:"&#1; 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white'>aaaa<br> </span></div> </layer><script>
+ mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.11 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='mso-line-spacing:"&#1; 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer><script>
+ mytop = 0.2 * 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 = 0.01 * 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:#E2EBF0'>D2 strain</span><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;display:none'><br> </span></div> </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%; 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></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:" 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:" 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="slide0017_image079.gif" 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:" 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:" 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 = 1.14 * 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 = 1.13 * 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%;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:Gadget;font-size:167%;color:white'>&gt;&gt;&gt;&gt;PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR &gt;&gt;&gt;&gt;&gt;</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="slide0017_image080.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.39 * g_height; myleft = 0.1 * g_width; myheight = 0.12 * g_height; mywidth = 0.03 * 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 = 0.05 * g_height; mywidth = 0.03 * 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:Palatino;font-size:233%; color:white'><b>&#4;<br> </b></span></div> </layer><script>
+ mytop = 0.06 * 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='text-align:center;mso-line-spacing:" 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 = 0.17 * g_width; myheight = 0.12 * g_height; mywidth = 0.03 * 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 = 0.05 * g_height; mywidth = 0.03 * 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:Palatino;font-size:233%; color:white'><b>&#4;<br> </b></span></div> </layer><script>
+ mytop = 0.06 * 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='text-align:center;mso-line-spacing:" 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="slide0017_image081.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.35 * g_height; myleft = 0.17 * g_width; myheight = 0.12 * g_height; mywidth = 0.03 * 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 = 0.05 * g_height; mywidth = 0.03 * 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:Palatino;font-size:233%; color:white'><b>&#4;<br> </b></span></div> </layer><script>
+ mytop = 0.06 * 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='text-align:center;mso-line-spacing:" 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 = 0.35 * g_height; myleft = 0.1 * g_width; myheight = 0.12 * g_height; mywidth = 0.03 * 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 = 0.05 * g_height; mywidth = 0.03 * 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:Palatino;font-size:233%; color:white'><b>&#4;<br> </b></span></div> </layer><script>
+ mytop = 0.06 * 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='text-align:center;mso-line-spacing:" 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 = 0.37 * g_height; myleft = 0.2 * g_width; myheight = 0.12 * g_height; mywidth = 0 * 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 * 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:Palatino;font-size:233%; color:white;display:none'><b><br> </b></span></div> </layer><script>
+ mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0 * 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:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script>
+ mytop = 0.27 * g_height; myleft = 0.04 * 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 language=JavaScript><!--
+xx = 0.04 * g_width;
+yy = 0.27 * g_height;
+ht = 0.21 * g_height;
+wd = 0.21 * g_width;
+document.write(
+'<img border=0 src="slide0017_image082.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.27 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * 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 = 0.1 * 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 = 0.05 * g_height; mywidth = 0.19 * 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:200%;color:#E9EB5D'><i>trans 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 = 0.16 * 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-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </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>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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun: yes">&nbsp; </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> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0050.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0050.htm
new file mode 100755
index 00000000..3c2f20c7
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+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Jun-19-03: WebQTL to exploring upstream control"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script>
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+'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.02 * g_height; myleft = 0.04 * g_width; myheight = 0.09 * g_height; mywidth = 1.05 * 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 = 1.03 * 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 &#1;";mso-line-spacing:" 0 &#1;"'><span style='font-family:Verdana;font-size:73%'><i>WebQTL to exploring upstream control</i></span></div> </layer></div> </layer><script>
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+</script></div> </layer><script>
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+</script> <div><script language=JavaScript><!--
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+</script></div> </layer><script>
+ mytop = 0.16 * g_height; myleft = 0.74 * 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 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">&nbsp; </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">&nbsp; </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
new file mode 100755
index 00000000..39d20b2b
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0051.htm
@@ -0,0 +1,127 @@
+<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> <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 to exploring upstream control."> <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>
+function font_size() {
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+ LoadNavSld("slide0051.htm");
+}//-->
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+wd = g_width;
+document.write(
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+</script></div> </layer><script>
+ mytop = 0.02 * g_height; myleft = 0.04 * g_width; myheight = 0.09 * g_height; mywidth = 1.06 * 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 = 0.07 * 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:" 0 &#1;";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:" 0 &#1;";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:73%'><i>WebQTL to exploring upstream control.</i></span></div> </layer></div> </layer><script>
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+</script> <div><script language=JavaScript><!--
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+'<img border=0 src="slide0019_image085.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.13 * g_height; myleft = 0.19 * g_width; myheight = 0.06 * g_height; mywidth = 0.6 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+//-->
+</script></div> </layer><script>
+ mytop = 0.82 * g_height; myleft = 0.26 * g_width; myheight = 0.14 * g_height; mywidth = 0.9 * 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 = 0.75 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><span style='font-size:267%;color:#E9EB5D'><i>Is App modulated by Chr 2?<br> </i></span></div> </layer><script>
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+</script> <div><span style='font-size:267%;color:#E9EB5D'><i>Probably, but donÕt bet the farm. </i></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=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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </span>peaks at a value<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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() {
+
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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>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">&nbsp; </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> </layer> <script language=JavaScript><!--
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+ 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>candidates</i></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="Times New Roman" size=4><b>Candidate Genes: </b><span style="mso-spacerun: yes">&nbsp;</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">&nbsp; </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> </layer> <script language=JavaScript><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
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new file mode 100755
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><span style='font-size:200%;color:#E9EB5D'><i>Hars2 = 0610006H08Rik<br> </i></span></div> </layer><script>
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+</script><span 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> </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>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">&nbsp; </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> </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/slide0055.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0055.htm
new file mode 100755
index 00000000..36b2d736
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+ window.location.replace( "endshow.htm" );
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+wd = g_width;
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+</script></div> </layer><script>
+ mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.08 * 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 = 0.06 * g_height; mywidth = 1.02 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+</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:"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> </layer><script>
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+</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:117%;color:#003399;mso-color-index: 4'><i>no SNPs</i></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=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">&nbsp; </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">&nbsp; </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> </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/slide0056.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0056.htm
new file mode 100755
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'><i>Cerebellum</i></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>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
new file mode 100755
index 00000000..9a7adf61
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+if ( ! top.PPTPRESENTATION ) {
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+wd = g_width;
+document.write(
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+</script></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script>
+ mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.06 * 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 &#1;";mso-margin-left-alt:232; mso-text-indent-alt:0;mso-line-spacing:" 0 &#1;";mso-margin-left-alt:232; mso-text-indent-alt:0'><span style='font-size:68%'><i>Is there known biology to link Hars2 with App? </i></span></div> </layer></div> </layer><script>
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+</script> <div></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
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+</script></div> </layer><script>
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+</script></div> </layer><script>
+ mytop = 0.14 * g_height; myleft = 0.69 * g_width; myheight = 0.06 * g_height; mywidth = 0.23 * 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:250%; color:#E9EB5D'><i><span style="mso-spacerun: yes">&nbsp;</span>Not obvious</i></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=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> </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/slide0058.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0058.htm
new file mode 100755
index 00000000..9feed242
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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>Part 3.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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><!--
+function playList() {
+
+}
+//-->
+</script> </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
new file mode 100755
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 &#1;";mso-line-spacing:" 0 &#1;"'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>other traits.</i></span></span></layer></div> </layer></div> </LAYER>
+ <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Genes must be polymorphic to generate downstream genetic effects (as opposed to downstream molecular effects). Hars2 meets this condition because we have already mapped a functional polymorphism in the gene. We can therefore posit that Hars2 is a QT gene. What transcripts are downstream? <i>App</i> is one obvious candidate, but there are many more.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The are several ways to look for downstream targets. The best and most obvious is to look up all transcripts that have high correlations with Hars2 itself. You should know how to do this. An alternative method is shown here for teaching purpose and to show you what to do if your gene of interest is not in our database. You need to know:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Times size=3>1.</font><font face=Verdana size=3> Where your gene is located. You need this information to find a surrogate marker; a marker that is located very close to your gene of interest.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. That your gene is polymorphic between C57BL/6J and DBA/2J.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>LetÕs look at the correlation of Hars2 with BXD genotypes as shown in the slide above to illustrate how to use markers as surrogate traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Go to the Trait Date and Editing window one more time. We want the data for Hars2 this time, not App. You should be able to show that Hars2 has a high<span style="mso-spacerun: yes">&nbsp; </span>correlation with D2Mit423 as shown in the slide above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>By clicking on the symbol D2Mit423 in the Correlation window, you will generate a new Trait Data window shown on the next slide.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm
new file mode 100755
index 00000000..aa804b9a
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+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0060.htm
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+wd = g_width;
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+ mytop = -0.01 * 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 + ' >' );
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+ mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.08 * g_width;
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+</script></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
+ mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.13 * 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>B = -1<br> </i></span></div> </layer><script>
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+</script> <div><span style='font-family:"Gill Sans";font-size:267%;color:#E9EB5D'><i>D = 1</i></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=Verdana size=3>We can review the set of correlations between the marker D2Mit423 and all transcripts in forebrain.<span style="mso-spacerun: yes">&nbsp; </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><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0061.htm
new file mode 100755
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+wd = g_width;
+document.write(
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+</script></div> </layer><script>
+ mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.11 * g_height; mywidth = 0.96 * g_width;
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+ 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; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 &#1;";mso-line-spacing:" 0 &#1;"'><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>
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+</script></div> </layer><script>
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+</script> <div><script>
+ mytop = 0.03 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 1.09 * 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 &#1;";mso-line-spacing:" 0 &#1;"'><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>
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+//-->
+</script></div> </layer><script>
+ mytop = 0.24 * g_height; myleft = 0.27 * g_width; myheight = 0.04 * 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%'><span style='font-size:150%;color:#FF0F0F'><b>Click here</b></span></div> </layer><script>
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+yy = 0.39 * g_height;
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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>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">&nbsp; </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> </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/slide0062.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0062.htm
new file mode 100755
index 00000000..c8c24f70
--- /dev/null
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+ht = g_height;
+wd = g_width;
+document.write(
+'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.11 * g_height; mywidth = 0.96 * 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 = 0.95 * 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; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 &#1;";mso-line-spacing:" 0 &#1;"'><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>
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+</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:233%; color:#E9EB5D'><i>modest support that Actn2 is modulated by the Hars2 region</i></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>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> </layer> <script language=JavaScript><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+ var size = 11 * g_width / g_origWidth;
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+ht = g_height;
+wd = g_width;
+document.write(
+'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = -0.01 * g_height; myleft = 0.02 * g_width; myheight = 0.09 * g_height; mywidth = 0.95 * 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 = 0.06 * 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 &#1;";mso-line-spacing:" 0 &#1;"'><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> </layer></div> </layer><script>
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+yy = 0.07 * g_height;
+ht = 0.28 * g_height;
+wd = 0.47 * g_width;
+document.write(
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+//-->
+</script></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.33 * g_width;
+yy = 0.17 * g_height;
+ht = 0.15 * g_height;
+wd = 0.15 * g_width;
+document.write(
+'<img border=0 src="slide0031_image118.gif" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.41 * g_height; myleft = 0.02 * g_width; myheight = 0.42 * g_height; mywidth = 0.28 * 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 = 0.26 * 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 + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>including 2 </i></span></span></layer><script>
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+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>actins, but not </i></span></span></layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>to Actn2 </i></span></span></layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:267%; color:#E9EB5D'><i>specifically.</i></span></span></layer></div> </layer><script>
+ mytop = 0.16 * g_height; myleft = 0.52 * g_width; myheight = 0.06 * g_height; mywidth = 0.25 * 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:267%; color:#E9EB5D'><i>Sort by gene</i></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>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">&nbsp; </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> </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/slide0064.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0064.htm
new file mode 100755
index 00000000..f75dd8f4
--- /dev/null
+++ b/web/tutorial/ppt/WebQTLDemo_files/slide0064.htm
@@ -0,0 +1,100 @@
+<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> <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:"> <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>
+function font_size() {
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+ if ( min > window.innerHeight/20 )
+ min = window.innerHeight/20;
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+function restore() {
+ self.location.reload();
+}
+function set_size() {
+ document.SlideLayer.width = window.innerWidth;
+ document.SlideLayer.height = window.innerHeight;
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+document.captureEvents(Event.MOUSEDOWN);
+document.captureEvents(Event.KEYPRESS);
+document.onkeypress = _KPH ;
+document.onmousedown = _KPH ;
+ parent.base.highlite();
+</script><script language=JavaScript><!--
+function DoOnLoad() {
+ LoadNavSld("slide0064.htm");
+}//-->
+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script>
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+ g_width = g_origWidth * g_height / g_origHeight;
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+g_top = (window.innerHeight - g_height) / 2;
+g_left = (window.innerWidth - g_width) / 2;
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+</script> <div><script language=JavaScript><!--
+ht = g_height;
+wd = g_width;
+document.write(
+'<img src="master03_background.gif" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.02 * g_height; myleft = 0.02 * 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><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 &#1;";mso-line-spacing:" 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> </layer><script>
+ mytop = 0.12 * g_height; myleft = 0.06 * g_width; myheight = 0.32 * g_height; mywidth = 0.9 * g_width;
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+</script> <div><script>
+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.32 * g_height; mywidth = 0.87 * g_width;
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+</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:" 0 &#1;";mso-line-spacing:" 0 &#1;"'><script>
+ 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%'>kenneth.manly@roswellpark.org<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;
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+</script><span style='text-align:left'><span style='font-size:82%'>lulu@ nb.utmem.edu<br> </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 style='text-align:left'><span style='font-size:82%'>echesler@ nb.utmem.edu</span></span></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=Verdana size=3>END</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/slide0065.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0065.htm
new file mode 100755
index 00000000..df6b13dd
--- /dev/null
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+ if ( parent.base.msie < 0 ) {
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+<script language=JavaScript>
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+ parent.base.highlite();
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+ </script><script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0066.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0066.htm
new file mode 100755
index 00000000..d0a85cac
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
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+ window.location.replace( "endshow.htm" );
+}
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+}
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+<script language=JavaScript>
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+ parent.base.SldUpdated( "slide0068.htm" );
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+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+ window.location.replace( "endshow.htm" );
+}
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+ document.captureEvents(Event.MOUSEDOWN);
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+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+ parent.base.SldUpdated( "slide0069.htm" );
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+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
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+ document.captureEvents(Event.MOUSEDOWN);
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+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+ parent.base.SldUpdated( "slide0070.htm" );
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+ </script><script language=JavaScript><!--
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
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+ document.captureEvents(Event.MOUSEDOWN);
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ parent.base.SldUpdated( "slide0071.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0007.gif border=0 usemap="#Slide0007.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
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+ document.onmousedown = _KPH;
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
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+ self.focus();
+ parent.base.SldUpdated( "slide0072.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0008.gif border=0 usemap="#Slide0008.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
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+ document.onmousedown = _KPH;
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
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+ self.focus();
+ parent.base.SldUpdated( "slide0073.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0009.gif border=0 usemap="#Slide0009.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
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+ document.onmousedown = _KPH;
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0074.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0010.gif border=0 usemap="#Slide0010.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+ document.captureEvents(Event.MOUSEDOWN);
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+ document.onmousedown = _KPH;
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
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+ self.focus();
+ parent.base.SldUpdated( "slide0075.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0011.gif border=0 usemap="#Slide0011.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
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+ document.onmousedown = _KPH;
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
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+ self.focus();
+ parent.base.SldUpdated( "slide0076.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0012.gif border=0 usemap="#Slide0012.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
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+ document.captureEvents(Event.MOUSEDOWN);
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+function restore() {
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+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ parent.base.SldUpdated( "slide0077.htm" );
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+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0013.gif border=0 usemap="#Slide0013.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
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+ document.captureEvents(Event.MOUSEDOWN);
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+ window.location.replace( "endshow.htm" );
+}
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+}
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+ parent.base.SldUpdated( "slide0080.htm" );
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+function DoOnLoad() {
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+ window.location.replace( "endshow.htm" );
+}
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+}
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+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.SldUpdated( "slide0081.htm" );
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+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0017.gif border=0 usemap="#Slide0017.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
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+}
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+}
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+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
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+ </script><script language=JavaScript><!--
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0018.gif border=0 usemap="#Slide0018.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Jun-19-03: WebQTL to exploring upstream control."> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
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+ document.captureEvents(Event.MOUSEDOWN);
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ self.focus();
+ parent.base.SldUpdated( "slide0083.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0019.gif border=0 usemap="#Slide0019.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Jun-19-03: The whole neighborhood is modulated!"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
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+ document.captureEvents(Event.MOUSEDOWN);
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+ document.onmousedown = _KPH;
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0084.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0020.gif border=0 usemap="#Slide0020.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Jun-19-03: Which gene is the QTL?"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
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+ document.onmousedown = _KPH;
+ }
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0085.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0021.gif border=0 usemap="#Slide0021.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
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+ document.onmousedown = _KPH;
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0086.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0022.gif border=0 usemap="#Slide0022.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jun-19-03> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
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+ document.captureEvents(Event.MOUSEDOWN);
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+ document.onmousedown = _KPH;
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0087.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0023.gif border=0 usemap="#Slide0023.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/WebQTLDemo_files/slide0088.htm b/web/tutorial/ppt/WebQTLDemo_files/slide0088.htm
new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+ document.captureEvents(Event.MOUSEDOWN);
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+function restore() {
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+ self.location.reload();
+}
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+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
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+ self.focus();
+ parent.base.SldUpdated( "slide0088.htm" );
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+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0024.gif border=0 usemap="#Slide0024.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+ self.location.reload();
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+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ parent.base.SldUpdated( "slide0089.htm" );
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+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0025.gif border=0 usemap="#Slide0025.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Jun-19-03: WebQTL link to www.webqtl.org/search.html"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
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new file mode 100755
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Binary files differ
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Binary files differ
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new file mode 100755
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new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/Slide0030.gif b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/Slide0030.gif
new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/Slide0031.gif b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/Slide0031.gif
new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/blank_notes.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/blank_notes.htm
new file mode 100755
index 00000000..4be5a447
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/blank_notes.htm
@@ -0,0 +1,5 @@
+<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 topmargin=0 leftmargin=0> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/endshow.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/endshow.htm
new file mode 100755
index 00000000..1ada008c
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/endshow.htm
@@ -0,0 +1 @@
+<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"> </head> <body bgcolor=black> <center> <p><font face=Arial color=white size=2><br> <b>Open the default .htm file to view this Web presentation.</b></font></p> </center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/error.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/error.htm
new file mode 100755
index 00000000..7444866d
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/error.htm
@@ -0,0 +1 @@
+<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"> </head> <body bgcolor=black> <center> <p><font face=Arial color=white size=2><br> <b>This presentation contains content that your browser is unable to display. This presentation was optimized for the recent version of Microsoft Internet Explorer and Netscape Navigator 4.</b></font></p> </center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/filelist.xml b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/filelist.xml
new file mode 100755
index 00000000..403bf8d7
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/filelist.xml
@@ -0,0 +1 @@
+<xml xmlns:o="urn:schemas-microsoft-com:office:office"> <o:File HRef="master03.htm"/> <o:File HRef="master05.htm"/> <o:File HRef="master02.htm"/> <o:File HRef="slide0001.htm"/> <o:File HRef="master03_background.png"/> <o:File HRef="slide0001_image001.png"/> <o:File HRef="slide0001_image002.png"/> <o:File HRef="slide0002.htm"/> <o:File HRef="master05_background.png"/> <o:File HRef="slide0002_image003.png"/> <o:File HRef="slide0002_image004.png"/> <o:File HRef="slide0002_image005.png"/> <o:File HRef="slide0002_image006.png"/> <o:File HRef="slide0002_image007.png"/> <o:File HRef="slide0002_image008.png"/> <o:File HRef="slide0002_image009.png"/> <o:File HRef="slide0002_image010.png"/> <o:File HRef="slide0002_image011.png"/> <o:File HRef="slide0002_image012.png"/> <o:File HRef="slide0002_image013.png"/> <o:File HRef="slide0002_image014.png"/> <o:File HRef="slide0002_image015.png"/> <o:File HRef="slide0002_image016.png"/> <o:File HRef="slide0002_image017.png"/> <o:File 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HRef="notes_flag.gif"/> <o:File HRef="fullscr.gif"/> <o:File HRef="fullscrClose.gif"/> <o:File HRef="narration.gif"/> <o:File HRef="navbg.gif"/> <o:File HRef="outline.gif"/> <o:File HRef="space.gif"/> <o:File HRef="blank_notes.htm"/> <o:File HRef="endshow.htm"/> <o:File HRef="navigation_bar.htm"/> <o:File HRef="fullscreen.htm"/> <o:File HRef="fs_navigation_bar.htm"/> <o:File HRef="outline_navigation_bar.htm"/> <o:File HRef="outline_collapsed.htm"/> <o:File HRef="outline_expanded.htm"/> <o:File HRef="slide0001_notes_pane.htm"/> <o:File HRef="slide0002_notes_pane.htm"/> <o:File HRef="slide0003_notes_pane.htm"/> <o:File HRef="slide0004_notes_pane.htm"/> <o:File HRef="slide0005_notes_pane.htm"/> <o:File HRef="slide0006_notes_pane.htm"/> <o:File HRef="slide0007_notes_pane.htm"/> <o:File HRef="slide0008_notes_pane.htm"/> <o:File HRef="slide0009_notes_pane.htm"/> <o:File HRef="slide0010_notes_pane.htm"/> <o:File HRef="slide0011_notes_pane.htm"/> <o:File HRef="slide0014_notes_pane.htm"/> 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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/frame.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/frame.htm
new file mode 100755
index 00000000..5aa0f55d
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/frame.htm
@@ -0,0 +1,43 @@
+<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"> <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"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script><script language=JavaScript><!--
+base = parent;//-->
+</script><script language=JavaScript src=script.js></script> </head> <script> <!--
+function getSlideName() {
+ return parent.GetHrefObj( parent.g_currentSlide ).m_slideHref;
+}
+
+function getNotesName() {
+ return parent.GetHrefObj( parent.g_currentSlide ).m_notesHref;
+}
+
+function restore() {
+ self.location.reload();
+}
+
+function WriteMe() {
+ if ( true )
+ document.write( '<frameset cols=\"20%,*\" id=PPTHorizAdjust >' +
+ '<frame src=\"outline_collapsed.htm\" name=PPTOtl>' );
+ var distribution;
+ if ( parent.includeNotes )
+ distribution = "*,20%";
+ else
+ distribution = "*,0";
+ document.write('<frameset rows=\"' + distribution + '\" id=PPTVertAdjust >' +
+ '<frame src=' + getSlideName() + ' name=PPTSld>' +
+ '<frame src=' + getNotesName() + ' name=PPTNts>' );
+ document.write('</frameset>');
+ if ( true )
+ document.write(' </frameset>' );
+}
+
+if ( parent.msie < 0 ) {
+ self.onresize = restore;
+}
+
+WriteMe();
+//-->
+</script> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fs_navigation_bar.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fs_navigation_bar.htm
new file mode 100755
index 00000000..8f728017
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fs_navigation_bar.htm
@@ -0,0 +1,84 @@
+<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> <title>Navigation Bar</title>
+<script>
+<!--
+function restore() {
+if( navigator.platform != "MacPPC" )
+ self.location.reload();
+}
+ mainWin = parent.base;
+ dad = parent;
+function WriteBody()
+{
+ if( window.name != "PPTNav" ) return;
+
+ document.writeln( '<table border=0 valign=top cellpadding=0 cellspacing=0 height=100% width=100%> <tr> <td align=center valign=top> <table border=0 valign=top cellpadding=0 cellspacing=0 height=100%><tr><td align=right valign=top>' );
+ if ( dad.g_hideNav != 1 ) {
+ innerText = "";
+ if ( mainWin.GetHrefObj( mainWin.g_currentSlide ).m_origVisibility == 1 && !mainWin.g_allHidden)
+ innerText = "Slide " + mainWin.GetCurrentSlideNum() + " of " + mainWin.GetNumSlides();
+ else
+ innerText = "Hidden Slide";
+ if( dad.gIsEndShow )
+ innerText = "End of Slide Show";
+
+fEnable = dad.M_HasPrevSld();
+ if( false || fEnable )
+ {
+ prevBtn = "prev_active.gif";
+ document.write( '<a onclick="if(event) event.cancelBubble=true" href="javascript:dad.M_GoPrevSld()" >' );
+ }
+ else
+ prevBtn = "prev_disabled.gif";
+
+ document.write( '<img src="' + prevBtn + '" border=0 alt="Previous Slide" title="Previous Slide">' );
+
+var textAlign;
+ if ( false )
+ textAlign = 'top';
+ else
+ textAlign = 'center';
+
+ if( false || fEnable )
+ document.write( '</a>' );
+
+ document.write( '</td><td align=center valign=' + textAlign + '> &nbsp &nbsp <font face=\"Arial\" color=#000000 size=2>' + innerText + '</font> &nbsp &nbsp </td><td align=left valign=top>' );
+
+
+fEnable = (!dad.gIsEndShow && mainWin.EndSlideShow) || (!mainWin.EndSlideShow &&( mainWin.GetCurrentSlideNum() != mainWin.GetNumSlides() ) );
+ if( false || fEnable )
+ {
+ nextBtn = "next_active.gif";
+ document.write( '<a onclick="if(event) event.cancelBubble=true" href="javascript:dad.M_GoNextSld()" >' );
+ }
+ else
+ nextBtn = "next_disabled.gif";
+ document.write( '<img src="' + nextBtn + '" border=0 alt="Next Slide" title="Next Slide">' );
+
+ if( false || fEnable )
+ document.write( '</a>' );
+ document.write( '</td> </tr></table> </td> <td align=right valign=top>' );
+ document.write( '<a onclick="if(event) event.cancelBubble=true" href="javascript:mainWin.CloseFullScreen()" > ' );
+ document.write( '<img src="fullscrClose.gif"border=0 alt="Close" title="Close">');
+ document.write( ' </a>' );
+ }
+ document.write( '</td> </tr></table>' );
+}
+if ( mainWin.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.onmousedown = handleClick;
+}
+
+function handleClick(event) {
+ if ( event.which == 3 )
+ return false;
+ return true;
+}
+//-->
+</script>
+ </head> <body background=navbg.gif topmargin=2 onresize="restore()" scroll="no" onkeypress="parent.processNavKPH(event)" onclick="parent.processNavClick()"oncontextmenu="parent.processNavClick(); return false"> <center><script language=JavaScript><!--
+WriteBody();//-->
+</script></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscr.gif b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscr.gif
new file mode 100755
index 00000000..85842700
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscr.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscrClose.gif b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscrClose.gif
new file mode 100755
index 00000000..ccd0de13
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscrClose.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscreen.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscreen.htm
new file mode 100755
index 00000000..8cfab86e
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/fullscreen.htm
@@ -0,0 +1,48 @@
+<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 ( ! opener.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script><script language=JavaScript src=script.js></script><script language=JavaScript><!--
+var SCREEN_MODE = "FullScreen";
+ base = self;
+ g_fullscrMode = 1;LoadHTMLVersion();
+//-->
+</script> </head> <script> <!--
+closing = false;
+PPTPRESENTATION = 1;
+function getSlideName() {
+ return opener.GetHrefObj( g_currentSlide ).m_slideHref;
+}
+function initpopup() {
+ if ( base.msie < 0 )
+ NavPopup = window.open( "fs_navigation_bar.htm", "controls", "alwaysRaised=yes,WIDTH=300,HEIGHT=50");
+ else
+ NavPopup = window.open( "fs_navigation_bar.htm", "controls", "WIDTH=300,HEIGHT=50");
+ NavPopup.focus();
+}
+
+
+function WriteMe() {
+ document.write( '<frameset rows=\" *,35 \" frameborder=0> ' +
+ ' ' +
+ '<frame src=\"' + getSlideName() + '\" name=PPTSld marginheight=0 marginwidth=0 scrolling=no noresize> ' +
+ ' <frame src="fs_navigation_bar.htm" name=PPTNav marginheight=0 marginwidth=0 scrolling=no noresize> ' +
+ '</frameset>' );
+ window.focus();
+}
+
+function shutdown( ) {
+if ( ! closing )
+
+ if ( window.NavPopup && !window.NavPopup.closed )
+ window.NavPopup.close();
+}
+
+WriteMe();
+// initpopup();
+
+
+ self.onunload = shutdown;
+
+//-->
+</script> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master02.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master02.htm
new file mode 100755
index 00000000..b696e328
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master02.htm
@@ -0,0 +1,11 @@
+<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.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> <meta name=Robots content=NoIndex> <link rel=Stylesheet href="master03_stylesheet.css"> <script language=JavaScript src=script.js></script>
+<script>
+<!--
+ parent.location.href=document.all.item("Main-File").href
+//-->
+</script>
+ </head> <body> <div class=O style='text-align:right;position:absolute;top:.53%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black'><b>Memphis Microarray 2003</b></span></div> <div class=O style='position:absolute;top:97.52%;left:1.32%;width:42.64%; height:2.12%'><span style='color:black'><b>June 11, 2003, Rob Williams</b></span></div> <div class=O style='text-align:right;position:absolute;top:97.52%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black;mso-field-code:meta16'><b>Ü#Ý</b></span><span style='color:black;mso-special-format:lastCR'><b><br> </b></span></div> </body> </html> \ No newline at end of file
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+<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" );
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+</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 >&gt;</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">&nbsp;&nbsp; </span><br> link to www.genenetwork.org</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</ilayer>'); 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+<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 ) {
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+}
+</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 >&gt;</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">&nbsp;&nbsp; </span><br> link to www.genenetwork.org</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 study expression variation and genetic correlation (slides 2&#8211;17)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators (slides 18&#8211;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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>&quot;Summary of Part 2&quot;</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 >&gt;</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 >&gt;</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> \ No newline at end of file
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new file mode 100755
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+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_navigation_bar.htm
@@ -0,0 +1,37 @@
+<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><script language=JavaScript><!--
+
+function restore() {
+if( navigator.platform != "MacPPC" )
+ self.location.reload();
+}
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+function writebody() {
+
+ if ( parent.g_showoutline ) {
+ document.write('<table border=0 valign=top cellspacing=0 width=\"100%\">' +
+ '<tr valign=top><td align=left valign=top>' );
+ document.write( '<a href=\"javascript:parent.ToggleOutline()\" ><img src=\"outline.gif\" title=\"Show/Hide Outline\" alt=\"Show/Hide Outline\" border=0></a>' );
+ document.write( '</td>' );
+ if( parent.g_outline_href == parent.OUTLINE_EXPAND_HREF ) {
+ document.write( '<td align=right valign=top><a href=\"javascript:parent.CollapseOutline()\">' +
+ '<img src="outline_collapse.gif" title="Collapse Outline" alt="Collapse Outline" border=0>' +
+ '</a></td>');
+ } else {
+ document.write('<td align=right valign=top><a href=\"javascript:parent.ExpandOutline()\">' +
+ '<img src="outline_expand.gif" title="Expand Outline" alt="Expand Outline" border=0>' +
+ '</a></td>');
+ }
+ document.write("</tr></table>");
+ }
+ else {
+ document.write( '<table border=0 valign=top cellspacing=0 width=\"100%\"><td align=\"left\"><a href=\"javascript:parent.ToggleOutline()\" ><img border=0 src=\"outline.gif\" title=\"Show/Hide Outline\" alt=\"Show/Hide Outline\"></a></td></table>' );
+ }
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new file mode 100755
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new file mode 100755
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+function LoadSld( slideId )
+{
+ if( !g_supportsPPTHTML ) return
+ if( slideId )
+ parent.base.SldUpdated(slideId)
+ g_origSz=parseInt(SlideObj.style.fontSize)
+ g_origH=SlideObj.style.posHeight
+ g_origW=SlideObj.style.posWidth
+ g_scaleHyperlinks=(document.all.tags("AREA").length>0)
+ if ( IsWin("PPTSld") && !parent.IsFullScrMode() )
+ parent.base.highlite();
+ if( g_scaleHyperlinks )
+ InitHLinkArray()
+ if( g_scaleInFrame||(IsWin("PPTSld") && parent.IsFullScrMode() ) )
+ document.body.scroll="no"
+ _RSW()
+ if( IsWin("PPTSld") && (parent.IsFullScrMode() || CtxAlwaysOn ) ) {
+ document.oncontextmenu=parent._CM;
+ self.focus();
+
+ }
+}
+function MakeSldVis( fTrans )
+{
+ fTrans=fTrans && g_showAnimation
+ if( fTrans )
+ {
+ if( g_bgSound ) {
+ idx=g_bgSound.indexOf(",");
+ pptSound.src=g_bgSound.substr( 0, idx );
+ pptSound.loop= -(parseInt(g_bgSound.substr(idx+1)));
+ }
+ SlideObj.filters.revealtrans.Apply()
+ }
+ SlideObj.style.visibility="visible"
+ if( fTrans )
+ SlideObj.filters.revealtrans.Play()
+}
+function MakeNotesVis()
+{
+ if( !IsNts() ) return false
+ SlideObj.style.display="none"
+ nObj = document.all.item("NotesObj")
+ parent.SetHasNts(0)
+ if( nObj ) {
+ nObj.style.display=""
+ parent.SetHasNts(1)
+ }
+ return 1
+}
+function Redirect( frmId,sId )
+{
+ var str=document.location.hash,idx=str.indexOf('#')
+ if(idx>=0) str=str.substr(1);
+ if( window.name != frmId && ( sId != str) ) {
+ obj = document.all.item("Main-File")
+ window.location.href=obj.href+"#"+sId
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+ return 0
+}
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+function IsWin( name ) { return window.name == name }
+function IsNts() { return IsWin("PPTNts") }
+function IsSldOrNts() { return( IsWin("PPTSld")||IsWin("PPTNts") ) }
+function SupportsPPTAnimation() { return( navigator.platform == "Win32" && navigator.appVersion.indexOf("Windows")>0 ) }
+function SupportsPPTHTML()
+{
+ var appVer=navigator.appVersion, msie=appVer.indexOf( "MSIE " ), inex = appVer.indexOf( "Internet Explorer " ), ver=0
+ if( msie >= 0 )
+ ver=parseFloat( appVer.substring( msie+5, appVer.indexOf(";",msie) ) )
+ else if( inex >= 0 )
+ ver=parseFloat( appVer.substring( inex+18, appVer.indexOf(";",inex) ) )
+ else
+ ver=parseInt(appVer)
+
+ return( ver >= 4 )
+}
+var MHTMLPrefix = CalculateMHTMLPrefix();
+function CalculateMHTMLPrefix()
+{
+ if ( document.location.protocol == 'mhtml:') {
+ href=new String(document.location.href)
+ Start=href.indexOf('!')+1
+ End=href.lastIndexOf('/')+1
+ if (End < Start)
+ return href.substring(0, Start)
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+ return href.substring(0, End)
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+}
+
+function LoadNavSld(slideId) {
+playList();
+parent.createCM();
+ if( !g_supportsPPTHTML ) return
+ if( IsWin("PPTSld") && slideId )
+ parent.base.SldUpdated(slideId)
+ self.focus();
+
+}
+var hasNarration = false;
+function _RSW()
+{
+ if( !g_supportsPPTHTML || IsNts() ||
+ ( !g_scaleInFrame && (( window.name != "PPTSld" ) ) ) )
+ return
+
+ cltWidth=document.body.clientWidth
+ cltHeight=document.body.clientHeight
+ factor=(1.0*cltWidth)/g_origW
+ if( cltHeight < g_origH*factor )
+ factor=(1.0*cltHeight)/g_origH
+
+ newSize = g_origSz * factor
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+
+ s=SlideObj.style
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+ s.posHeight=g_origH*factor
+ s.posLeft=(cltWidth-s.posWidth)/2
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+ if ( hasNarration ) {
+ obj = document.all.NSPlay.style;
+ mySld = document.all.SlideObj.style;
+ obj.position = 'absolute';
+ obj.posTop = mySld.posTop + mySld.posHeight - 20;
+ obj.posLeft = mySld.posLeft + mySld.posWidth - 20;
+ }
+ if( g_scaleHyperlinks )
+ ScaleHyperlinks( factor );
+}
+function IsMac() {
+ return (window.navigator.platform.indexOf("Mac") >= 0 );
+}
+
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+ return (evt.which == 1 || (IsMac() && evt.which == 3) );
+}
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+ return parent.KPH(event);
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+ parent.PPTSld.DocumentOnClick();
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+ parent.M_GoNextSld();
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+ parent.M_GoNextSld();
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+ 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();
+}
+
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+{
+ 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;
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+function SetHasNts( fVal )
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+ if( gHasNts != fVal ) {
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+ UpdNavPane()
+ }
+}
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+ PPTSld.ToggleSound( false, PPTSld.document.NSPlay );
+ return;
+ }
+
+ rObj=PPTSld.document.all("NSPlay")
+ if( rObj ) {
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+ rObj.Play()
+ else
+ rObj.Pause()
+
+ gNarrationPaused=!gNarrationPaused
+ }
+}
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+function HasNextSld() { return (GetCurrentSlideNum() != GetNumSlides()) }
+function StartEndShow()
+{
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+// PPTNav.location.reload();
+ if( PPTSld.event ) PPTSld.event.cancelBubble=true
+
+ doc=PPTSld.document
+ doc.open()
+ doc.writeln('<html><head><script > /*defer>*/ g_ctxmenu = 0; ' +
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+ 'function DocumentOnClick(event) { return _KPH(event); } function IsContextMenu() { return (g_ctxmenu ==1); } ' +
+ 'function _KPH(event)' +
+ '{ ' +
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+ ' else if ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8) ) { parent.M_GoPrevSld(); } } ' +
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+ doc.close()
+}
+function SetSldVisited(){ gDocTable[gCurSld-1].mVisited=true }
+function IsSldVisited(){ return gDocTable[gCurSld-1].mVisited }
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+ this.mSldIdx = sldIdx
+ this.mOrigVis= this.mVis = visible
+ this.mVisited= false
+}
+var gDocTable = new Array(
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+ new hrefList("slide0014.htm", 1, 14)
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+ t.SetActive = _IBSetA
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+ t.SetPressed = _IBSetP
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+ t.Enabled = _IBSetE
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+ t.mBorderId= bId
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+}
+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( " > &nbsp " + 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;
+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
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm
new file mode 100755
index 00000000..11938baa
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm
@@ -0,0 +1,25 @@
+<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.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"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Aug-15-05: The GeneNetwork and WebQTL : PART 2 link to www.genenetwork.org"> <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="slide0001.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: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">&nbsp;&nbsp; </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&#8211;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&#8211;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> </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/slide0001_image001.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image001.png
new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image002.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image002.png
new file mode 100755
index 00000000..e06bd0db
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+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image002.png
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_notes_pane.htm
new file mode 100755
index 00000000..9e0445f3
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_notes_pane.htm
@@ -0,0 +1,5 @@
+<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=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> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002.htm
new file mode 100755
index 00000000..b40dd6e1
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002.htm
@@ -0,0 +1,25 @@
+<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.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"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master05_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 ) ) {
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+ document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref);
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+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="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">&nbsp; </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> <script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002_notes_pane.htm
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+<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>
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+</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 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">&nbsp; </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=2>Notes:</font><br> </td> </tr> <tr> <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> </tr> <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> \ No newline at end of file
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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%'><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'>&gt;&gt;&gt;&gt;PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR &gt;&gt;&gt;&gt;&gt;</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>&#4;</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>&#4;</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>&#4;</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>&#4;</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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun: yes">&nbsp; </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><!--
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+</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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun: yes">&nbsp; </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
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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%'><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">&nbsp; </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">&nbsp; </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><!--
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+<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>
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+</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">&nbsp; </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">&nbsp; </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> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005.htm
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+</script> <meta name=Description content="Aug-15-05: WebQTL searches for upstream controllers"> <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><!--
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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:-.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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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><!--
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+<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 ) {
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+</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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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
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+</script> <meta name=Description content="Aug-15-05: Genetic versus Physical maps for App expression"> <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><!--
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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:-.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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+<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>
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+</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
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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:-.53%;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%'>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%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <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" style='position:absolute;top:15.54%;left:6.62%;width:68.34%;height:75.61%'></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=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">&nbsp; </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> <script language=JavaScript><!--
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+</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>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">&nbsp; </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> \ No newline at end of file
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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%'><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)'> <div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:18.36%; 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">&nbsp;</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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp; </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> <script language=JavaScript><!--
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+</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>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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp; </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> \ No newline at end of file
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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:-.53%;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%'>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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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> <script language=JavaScript><!--
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+</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>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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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
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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: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">&nbsp; </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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> </div> <script language=JavaScript><!--
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+<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 ) {
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+</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">&nbsp; </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes">&nbsp; </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=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">&nbsp; </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> \ No newline at end of file
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+LoadSld( gId );
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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: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">&nbsp; </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">&nbsp; </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> <script language=JavaScript><!--
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+<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>
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+</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>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">&nbsp; </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">&nbsp; </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> \ No newline at end of file
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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:-.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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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> <script language=JavaScript><!--
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+<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 ) {
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+}
+</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
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Aug-15-05: Test Questions"> <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="slide0013.htm"
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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: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> <script language=JavaScript><!--
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+<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=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
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-size:73%'>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes">&nbsp;&nbsp; </span><br> </span></span></layer><script>
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image034.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image034.png
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_notes_pane.htm
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+<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>
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+</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
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+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016.htm
@@ -0,0 +1,919 @@
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+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 + ' >' );
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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>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">&nbsp; </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> </layer> <script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_image036.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_image036.png
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_notes_pane.htm
new file mode 100755
index 00000000..f5776dad
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_notes_pane.htm
@@ -0,0 +1,5 @@
+<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>
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+</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
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+ mytop = 0.01 * 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:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 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> </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:"-384 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:"-384 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:"-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> </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="slide0003_image056.png" 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="slide0003_image057.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.2 * g_height; myleft = 0.38 * g_width; myheight = 0.26 * g_height; mywidth = 0.3 * 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 = 0.23 * 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="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 + ' >' );
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+//-->
+</script></div> </layer><script>
+ mytop = 0.27 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.2 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+</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>trans QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script>
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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>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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun: yes">&nbsp; </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><!--
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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">&nbsp; </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">&nbsp; </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><!--
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+<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>
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+</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: 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> \ No newline at end of file
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script>
+ mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * 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>
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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>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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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> <script language=JavaScript><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
+//-->
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+</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 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">&nbsp; </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=2>Notes:</font><br> </td> </tr> <tr> <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> </tr> <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> \ No newline at end of file
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-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>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> </layer></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span 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>
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+</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><!--
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+<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 ) {
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+</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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun: yes">&nbsp; </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
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+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * 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 = 0.06 * 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> </layer><script>
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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>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">&nbsp; </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> <script language=JavaScript><!--
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+</script><script language=JavaScript><!--
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+
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+</script> </body> </html> \ No newline at end of file
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+<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>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">&nbsp; </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">&nbsp; </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> \ No newline at end of file
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+ mytop = -0.01 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.93 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.91 * 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"'><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> </layer></div> </layer><script>
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+ mytop = 0.03 * g_height; myleft = 0.69 * g_width; myheight = 0.17 * g_height; mywidth = 0.33 * g_width;
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
+ 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> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <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 + ' >' );
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+ mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 0.21 * g_width;
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+ 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>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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp; </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> </layer> <script language=JavaScript><!--
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+<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>
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+</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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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
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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>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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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><!--
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+<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 ) {
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+</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
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+ 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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;color:#E9EB5D'><i> the App QTL </i></span></span></layer><script>
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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>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">&nbsp; </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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> </div> </layer> <script language=JavaScript><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
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+</script> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image109.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image109.png
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_notes_pane.htm
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+<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>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 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">&nbsp; </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> \ No newline at end of file
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script>
+ mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * 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%'>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> </layer></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.19 * g_width;
+yy = 0.4 * g_height;
+ht = 0.54 * g_height;
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+document.write(
+'<img border=0 src="slide0011_image088.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=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">&nbsp; </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">&nbsp; </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> </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/slide0025_image112.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image112.png
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+<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 ) {
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+}
+</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>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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp; </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> \ No newline at end of file
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+ 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 2</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>
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+</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 = 0.04 * 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">&nbsp;</span>Covered the basics of QTL analysis and mapping.<br> </span></span></layer></div> </layer><script>
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+ 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 + ' >' );
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+</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 = 0.98 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>the additive effect function, the bootstrap bars, and the permutation </span></span></layer><script>
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+</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 = 0.86 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+</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 + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
+ 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>
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+</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>
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+</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>
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+</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>
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+</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> </layer></div> </LAYER>
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+</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>Even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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
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+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * g_width;
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-size: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>
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+<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 ) {
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+}
+</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">&nbsp; </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'>kmanly@utmem.edu</span></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image123.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image123.png
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+<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>
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+</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>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </span>with several transcription factors including EVI1, ZFPM1, and<span style="mso-spacerun: yes">&nbsp;&nbsp; </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> </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 signalling. To estabilish this common gene ontology visit NCBI<span style="mso-spacerun: yes">&nbsp; </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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> </body> </html> \ No newline at end of file
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.9 * 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: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> </layer></div> </layer><script>
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+//-->
+</script><script language=JavaScript><!--
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+
+}
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0044.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0044.htm
new file mode 100755
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+wd = g_width;
+document.write(
+'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * 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 = 0.96 * 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: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'> transcript and eight of its neighbors</span></div> </layer></div> </layer><script>
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+</script> <div><script language=JavaScript><!--
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+yy = 0.09 * g_height;
+ht = 0.9 * g_height;
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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>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.ppt_files/slide0045.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0045.htm
new file mode 100755
index 00000000..4e705866
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0045.htm
@@ -0,0 +1,118 @@
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+<script language=JavaScript>
+function font_size() {
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+}
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+}
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+document.captureEvents(Event.KEYPRESS);
+document.onkeypress = _KPH ;
+document.onmousedown = _KPH ;
+ parent.base.highlite();
+</script><script language=JavaScript><!--
+function DoOnLoad() {
+ LoadNavSld("slide0045.htm");
+}//-->
+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script>
+
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+
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+ht = g_height;
+wd = g_width;
+document.write(
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+//-->
+</script></div> </layer><script>
+ mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div></div> </layer><script>
+ mytop = -0.02 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 1.05 * 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 = 0.07 * g_height; mywidth = 1.04 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+</script> <div><script language=JavaScript><!--
+xx = 0.01 * g_width;
+yy = 0.37 * g_height;
+ht = 0.62 * g_height;
+wd = 0.97 * g_width;
+document.write(
+'<img border=0 src="slide0014_image029.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.11 * g_height; myleft = 0.01 * g_width; myheight = 0.25 * g_height; mywidth = 0.79 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.01 * g_width;
+yy = 0.11 * g_height;
+ht = 0.25 * g_height;
+wd = 0.79 * g_width;
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+//-->
+</script></div> </layer><script>
+ mytop = 0.1 * g_height; myleft = 0.81 * g_width; myheight = 0.09 * g_height; mywidth = 0.18 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.81 * g_width;
+yy = 0.1 * g_height;
+ht = 0.09 * g_height;
+wd = 0.18 * g_width;
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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">&nbsp; </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
new file mode 100755
index 00000000..93429543
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm
@@ -0,0 +1,104 @@
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jul-18-05> <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>
+function font_size() {
+ var min = window.innerWidth/20;
+ if ( min > window.innerHeight/20 )
+ min = window.innerHeight/20;
+
+ return min+"pt";
+}
+var SoundEnabled = navigator.plugins && navigator.plugins["LiveAudio"];
+function restore() {
+ self.location.reload();
+}
+function set_size() {
+ document.SlideLayer.width = window.innerWidth;
+ document.SlideLayer.height = window.innerHeight;
+}
+document.captureEvents(Event.MOUSEDOWN);
+document.captureEvents(Event.KEYPRESS);
+document.onkeypress = _KPH ;
+document.onmousedown = _KPH ;
+ parent.base.highlite();
+</script><script language=JavaScript><!--
+function DoOnLoad() {
+ LoadNavSld("slide0046.htm");
+}//-->
+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script>
+
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+</script> <div><script language=JavaScript><!--
+ht = g_height;
+wd = g_width;
+document.write(
+'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0 * g_height; myleft = 0 * 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'>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> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.04 * g_width;
+yy = 0.28 * g_height;
+ht = 0.7 * g_height;
+wd = 0.78 * g_width;
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+//-->
+</script></div> </layer><script>
+ mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.19 * g_height; mywidth = 0.33 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.04 * g_width;
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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.ppt_files/slide0047.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm
new file mode 100755
index 00000000..e7568e44
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm
@@ -0,0 +1,93 @@
+<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 href="webqtl_demo2.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
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+}
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+</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>
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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>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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+ 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 + ' >' );
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+ 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">&nbsp;</span>You have learned the basics about searching for traits<br> </span></span></layer></div> </layer><script>
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+ mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width;
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+</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 + ' >' );
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+ 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">&nbsp;</span>You know how to review the basic statistics of a trait<br> </span></span></layer></div> </layer><script>
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+ 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 + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>traits using the Traits Correlation tool<br> </span></span></layer></div> </layer><script>
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+</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 = 0.98 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+</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 + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>co-vary. </span></span></layer></div> </layer></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+}
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0050.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0050.htm
new file mode 100755
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+ mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.29 * 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:Times;font-size:117%; color:white;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script>
+ mytop = 0.02 * g_height; myleft = -0.05 * g_width; myheight = 0.11 * g_height; mywidth = 1.05 * 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 = 0.1 * 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 = 0.06 * g_height; mywidth = 1.05 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:center;mso-line-spacing:"-240 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16'><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> </layer><script>
+ mytop = 0.06 * g_height; myleft = 0.06 * g_width; myheight = 0.03 * g_height; mywidth = 0.92 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:center;mso-line-spacing:"-160 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16'><span style='font-family:Arial;font-size:150%; color:aqua;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </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="slide0019_image039.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="slide0019_image040.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="slide0019_image041.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="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><!--
+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="slide0019_image077.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="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 + ' >' );
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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>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">&nbsp; </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> </layer> <script language=JavaScript><!--
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+ 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'>&gt;&gt;&gt;&gt;PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR &gt;&gt;&gt;&gt;&gt;</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(
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+//-->
+</script></div> </layer><script>
+ mytop = 0.27 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.2 * 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 = 0.19 * 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 = 0.05 * g_height; mywidth = 0.19 * 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>trans QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script>
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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>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">&nbsp; </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">&nbsp;&nbsp; </span>a.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>b.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp;&nbsp; </span>c.<span style="mso-spacerun: yes">&nbsp; </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><!--
+//-->
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+
+}
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm
new file mode 100755
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+'<img border=0 src="slide0021_image099.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
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+</script></div> </layer><script>
+ mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.08 * g_height; mywidth = 0.93 * g_width;
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+</script> <div><script>
+ mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 0.91 * 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"'><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> </layer><script>
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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">&nbsp; </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">&nbsp; </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() {
+
+}
+//-->
+</script> </body> </html> \ 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
new file mode 100755
index 00000000..d729b467
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+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0053.htm
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+if ( ! top.PPTPRESENTATION ) {
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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>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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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> <script language=JavaScript><!--
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+</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 (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> </td> </tr> </table> </div> </layer> <script language=JavaScript><!--
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+</script><script language=JavaScript><!--
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+
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+//-->
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0055.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0055.htm
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+</script> <meta name=Description content="Jul-18-05: Physical map for distal chromosome 7"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=Javascript src=script.js></script>
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+wd = g_width;
+document.write(
+'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * 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 = 0.06 * 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>
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+ 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> </layer><script>
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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>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">&nbsp; </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> <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/slide0056.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0056.htm
new file mode 100755
index 00000000..eba3fc05
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+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0056.htm
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+<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 href="webqtl_demo2.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Jul-18-05: Evaluating candidate genes"> <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>
+function font_size() {
+ var min = window.innerWidth/20;
+ if ( min > window.innerHeight/20 )
+ min = window.innerHeight/20;
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+function DoOnLoad() {
+ LoadNavSld("slide0056.htm");
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+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script>
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+ mytop = -0.01 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.93 * g_width;
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+</script></div> </layer><script>
+ mytop = 0.03 * g_height; myleft = 0.69 * g_width; myheight = 0.17 * g_height; mywidth = 0.33 * 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 = 0.16 * 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> </layer><script>
+ mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.31 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <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> </layer></div> </layer><script>
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+ 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 = 0.21 * 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 = 0.07 * 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">&nbsp;</span></i></span><span style='font-size:200%; color:#E9EB5D'><i>= better<br> </i></span></div> </layer><script>
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+ 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>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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp; </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> </layer> <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=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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp; </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/slide0058.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm
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index 00000000..47e08c87
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+++ b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm
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+<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 href="webqtl_demo2.ppt.ppt"> <script>
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+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.06 * 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 = 0.06 * 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>
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+ 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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><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>
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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>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">&nbsp; </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes">&nbsp; </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=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">&nbsp; </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> </div> </layer> <script language=JavaScript><!--
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script>
+ mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.06 * 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%'>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> </layer></div> </layer><script>
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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>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </span>with several transcription factors including EVI1, ZFPM1, and<span style="mso-spacerun: yes">&nbsp;&nbsp; </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> </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 signalling. To estabilish this common gene ontology visit NCBI<span style="mso-spacerun: yes">&nbsp; </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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> </layer> <script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm
new file mode 100755
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ 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 2:</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>
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+ 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 + ' >' );
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ 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 = 0.95 * 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">&nbsp;</span>Discussed interpreting features of QTL maps including the </span></span></layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>LRS function, the additive effect function, the bootstrap bars, </span></span></layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>and the permutation thresholds.<br> </span></span></layer></div> </layer><script>
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+</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 = 1 * g_width;
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+ 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 = 0.94 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ 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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size: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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>quality and relevance of the phenotype and the statistical </span></span></layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>strength of the QTL. As usual, test and be skeptical.</span></span></layer></div> </layer></div> </LAYER>
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+//-->
+</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/slide0061.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0061.htm
new file mode 100755
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+</script></div> </layer><script>
+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.01 * 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 = 0.06 * 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%'>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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
+ 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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-size: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 = 0.45 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * 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 = 0.06 * 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 = 1.05 * 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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
+ 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>
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+</script> </body> </html> \ 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
new file mode 100755
index 00000000..6b671799
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
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+<script language=JavaScript>
+function font_size() {
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br> </span></span></layer><script>
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+}
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+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
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+}
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+<script language=JavaScript>
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+function DoOnLoad() {
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+ window.location.replace( "endshow.htm" );
+}
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+ self.location.reload();
+}
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+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
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+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ self.focus();
+ parent.base.SldUpdated( "slide0075.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0013.gif border=0 usemap="#Slide0013.gif_map"></center> </body> </html> \ No newline at end of file
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+ window.location.replace( "endshow.htm" );
+}
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+function restore() {
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+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+ self.focus();
+ parent.base.SldUpdated( "slide0076.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0014.gif border=0 usemap="#Slide0014.gif_map"></center> </body> </html> \ No newline at end of file
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+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
+
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ self.focus();
+ parent.base.SldUpdated( "slide0077.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0015.gif border=0 usemap="#Slide0015.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
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+ document.onmousedown = _KPH;
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+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0078.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0016.gif border=0 usemap="#Slide0016.gif_map"></center> </body> </html> \ No newline at end of file
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+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
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+ document.onmousedown = _KPH;
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+function restore() {
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+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ self.focus();
+ parent.base.SldUpdated( "slide0079.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0017.gif border=0 usemap="#Slide0017.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+ window.location.replace( "endshow.htm" );
+}
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+ if ( parent.base.msie < 0 ) {
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+function restore() {
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+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ self.focus();
+ parent.base.SldUpdated( "slide0080.htm" );
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+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0018.gif border=0 usemap="#Slide0018.gif_map"></center> </body> </html> \ No newline at end of file
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new file mode 100755
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+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
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+ document.onmousedown = _KPH;
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+function restore() {
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+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ self.focus();
+ parent.base.SldUpdated( "slide0081.htm" );
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+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0019.gif border=0 usemap="#Slide0019.gif_map"></center> </body> </html> \ No newline at end of file
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+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Jul-18-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
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+function restore() {
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+ self.location.reload();
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+</script>
+<script language=JavaScript>
+function flatLoad() {
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+ parent.base.highlite();
+DoOnLoad();
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+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
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+ parent.base.SldUpdated( "slide0082.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
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+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0020.gif border=0 usemap="#Slide0020.gif_map"></center> </body> </html> \ No newline at end of file
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+<html> <head> <meta name=Title content="PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics"> <meta name=Keywords content=OPA> <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 rel=Edit-Time-Data href="webqtl_demo2_part1.ppt_files/editdata.mso"> <link rel=OLE-Object-Data href="webqtl_demo2_part1.ppt_files/oledata.mso"> <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_files/webqtl_demo2_part1.ppt.ppt"> <meta http-equiv=expires content=0> <script language=JavaScript src="webqtl_demo2_part1.ppt_files/script.js"></script><script language=JavaScript><!--
+LoadHTMLVersion();
+ if (g_ShowFSDefault ) FullScreen();//-->
+</script> </head> <frameset rows="*,35" framespacing=1 frameborder=1> <noframes> <body> <p>This page uses frames, but your browser doesn't support them.</p> </body> </noframes> <frame src="webqtl_demo2_part1.ppt_files/frame.htm" name=MainFrame marginheight=0 marginwidth=0> <frameset cols="20%,*"> <frame src="webqtl_demo2_part1.ppt_files/outline_navigation_bar.htm" name=PPTOtlNav marginheight=0 marginwidth=0 scrolling=no noresize> <frame src="webqtl_demo2_part1.ppt_files/navigation_bar.htm" name=PPTNav marginheight=0 marginwidth=0 scrolling=no noresize> </frameset> </frameset> </html> \ No newline at end of file
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new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0004.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0004.gif
new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0005.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0005.gif
new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0006.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0006.gif
new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0007.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0007.gif
new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0008.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0008.gif
new file mode 100755
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+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0008.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0009.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0009.gif
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0010.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0010.gif
new file mode 100755
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Binary files differ
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new file mode 100755
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+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0012.gif
Binary files differ
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new file mode 100755
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+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0013.gif
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diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0014.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0014.gif
new file mode 100755
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+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0014.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0015.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0015.gif
new file mode 100755
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diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0016.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0016.gif
new file mode 100755
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Binary files differ
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new file mode 100755
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+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0017.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0018.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0018.gif
new file mode 100755
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Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0019.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0019.gif
new file mode 100755
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+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/Slide0019.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/blank_notes.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/blank_notes.htm
new file mode 100755
index 00000000..e833eefd
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/blank_notes.htm
@@ -0,0 +1,5 @@
+<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 topmargin=0 leftmargin=0> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/endshow.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/endshow.htm
new file mode 100755
index 00000000..a2ed520a
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/endshow.htm
@@ -0,0 +1 @@
+<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"> </head> <body bgcolor=black> <center> <p><font face=Arial color=white size=2><br> <b>Open the default .htm file to view this Web presentation.</b></font></p> </center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/error.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/error.htm
new file mode 100755
index 00000000..f2002169
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/error.htm
@@ -0,0 +1 @@
+<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"> </head> <body bgcolor=black> <center> <p><font face=Arial color=white size=2><br> <b>This presentation contains content that your browser is unable to display. This presentation was optimized for the recent version of Microsoft Internet Explorer and Netscape Navigator 4.</b></font></p> </center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/filelist.xml b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/filelist.xml
new file mode 100755
index 00000000..4a47f1fe
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/filelist.xml
@@ -0,0 +1 @@
+<xml xmlns:o="urn:schemas-microsoft-com:office:office"> <o:File HRef="master03.htm"/> <o:File HRef="master02.htm"/> <o:File HRef="slide0001.htm"/> <o:File HRef="master03_background.png"/> <o:File HRef="slide0001_image001.png"/> <o:File HRef="slide0002.htm"/> <o:File HRef="slide0002_image002.png"/> <o:File HRef="slide0002_image003.png"/> <o:File HRef="slide0002_image004.png"/> <o:File HRef="slide0003.htm"/> <o:File HRef="slide0003_image005.png"/> <o:File HRef="slide0003_image006.png"/> <o:File HRef="slide0003_image008.png"/> <o:File HRef="slide0003_image009.png"/> <o:File HRef="slide0004.htm"/> <o:File HRef="slide0004_image010.png"/> <o:File HRef="slide0004_image012.png"/> <o:File HRef="slide0005.htm"/> <o:File HRef="slide0005_image013.png"/> <o:File HRef="slide0005_image014.png"/> <o:File HRef="slide0006.htm"/> <o:File HRef="slide0006_image015.png"/> <o:File HRef="slide0007.htm"/> <o:File HRef="slide0007_image016.png"/> <o:File HRef="slide0007_image017.png"/> <o:File HRef="slide0008.htm"/> <o:File HRef="slide0008_image018.png"/> <o:File HRef="slide0008_image019.png"/> <o:File HRef="slide0008_image021.png"/> <o:File HRef="slide0009.htm"/> <o:File HRef="slide0009_image022.png"/> <o:File HRef="slide0010.htm"/> <o:File HRef="slide0010_image023.png"/> <o:File HRef="slide0010_image024.png"/> <o:File HRef="slide0011.htm"/> <o:File HRef="slide0011_image025.png"/> <o:File HRef="slide0012.htm"/> <o:File HRef="slide0012_image026.png"/> <o:File HRef="slide0013.htm"/> <o:File HRef="slide0013_image027.png"/> <o:File HRef="slide0014.htm"/> <o:File HRef="slide0014_image029.png"/> <o:File HRef="slide0014_image031.png"/> <o:File HRef="slide0014_image033.png"/> <o:File HRef="slide0015.htm"/> <o:File HRef="slide0015_image034.png"/> <o:File HRef="slide0015_image035.png"/> <o:File HRef="slide0016.htm"/> <o:File HRef="slide0016_image036.png"/> <o:File HRef="slide0017.htm"/> <o:File HRef="slide0018.htm"/> <o:File HRef="master03_stylesheet.css"/> <o:File HRef="slide0019.htm"/> <o:File HRef="slide0020.htm"/> <o:File HRef="slide0021.htm"/> <o:File HRef="slide0022.htm"/> <o:File HRef="slide0023.htm"/> <o:File HRef="slide0024.htm"/> <o:File HRef="slide0025.htm"/> <o:File HRef="slide0026.htm"/> <o:File HRef="slide0027.htm"/> <o:File HRef="slide0028.htm"/> <o:File HRef="slide0029.htm"/> <o:File HRef="slide0030.htm"/> <o:File HRef="slide0031.htm"/> <o:File HRef="slide0032.htm"/> <o:File HRef="slide0033.htm"/> <o:File HRef="slide0034.htm"/> <o:File HRef="slide0035.htm"/> <o:File HRef="slide0036.htm"/> <o:MainFile HRef="::webqtl_demo2_part1.ppt.htm"/> <o:File HRef="error.htm"/> <o:File HRef="frame.htm"/> <o:File HRef="next_active.gif"/> <o:File HRef="next_disabled.gif"/> <o:File HRef="prev_active.gif"/> <o:File HRef="prev_disabled.gif"/> <o:File HRef="outline_collapse.gif"/> <o:File HRef="outline_expand.gif"/> <o:File HRef="notes_flag.gif"/> <o:File HRef="fullscr.gif"/> <o:File HRef="fullscrClose.gif"/> <o:File HRef="narration.gif"/> <o:File HRef="navbg.gif"/> <o:File HRef="outline.gif"/> <o:File HRef="space.gif"/> <o:File HRef="blank_notes.htm"/> <o:File HRef="endshow.htm"/> <o:File HRef="navigation_bar.htm"/> <o:File HRef="fullscreen.htm"/> <o:File HRef="fs_navigation_bar.htm"/> <o:File HRef="outline_navigation_bar.htm"/> <o:File HRef="outline_collapsed.htm"/> <o:File HRef="outline_expanded.htm"/> <o:File HRef="slide0001_notes_pane.htm"/> <o:File HRef="slide0002_notes_pane.htm"/> <o:File HRef="slide0003_notes_pane.htm"/> <o:File HRef="slide0004_notes_pane.htm"/> <o:File HRef="slide0005_notes_pane.htm"/> <o:File HRef="slide0006_notes_pane.htm"/> <o:File HRef="slide0007_notes_pane.htm"/> <o:File HRef="slide0008_notes_pane.htm"/> <o:File HRef="slide0009_notes_pane.htm"/> <o:File HRef="slide0010_notes_pane.htm"/> <o:File HRef="slide0011_notes_pane.htm"/> <o:File HRef="slide0012_notes_pane.htm"/> <o:File HRef="slide0013_notes_pane.htm"/> <o:File HRef="slide0014_notes_pane.htm"/> <o:File HRef="slide0015_notes_pane.htm"/> <o:File HRef="slide0016_notes_pane.htm"/> <o:File HRef="slide0018_notes_pane.htm"/> <o:File HRef="slide0037.htm"/> <o:File HRef="slide0038.htm"/> <o:File HRef="slide0039.htm"/> <o:File HRef="slide0040.htm"/> <o:File HRef="slide0041.htm"/> <o:File HRef="slide0042.htm"/> <o:File HRef="slide0043.htm"/> <o:File HRef="slide0044.htm"/> <o:File HRef="slide0045.htm"/> <o:File HRef="slide0046.htm"/> <o:File HRef="slide0047.htm"/> <o:File HRef="slide0048.htm"/> <o:File HRef="slide0049.htm"/> <o:File HRef="slide0050.htm"/> <o:File HRef="slide0051.htm"/> <o:File HRef="slide0052.htm"/> <o:File HRef="slide0053.htm"/> <o:File HRef="slide0054.htm"/> <o:File HRef="script.js"/> <o:File HRef="filelist.xml"/> </xml> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/frame.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/frame.htm
new file mode 100755
index 00000000..2981fa86
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/frame.htm
@@ -0,0 +1,43 @@
+<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"> <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><script language=JavaScript><!--
+base = parent;//-->
+</script><script language=JavaScript src=script.js></script> </head> <script> <!--
+function getSlideName() {
+ return parent.GetHrefObj( parent.g_currentSlide ).m_slideHref;
+}
+
+function getNotesName() {
+ return parent.GetHrefObj( parent.g_currentSlide ).m_notesHref;
+}
+
+function restore() {
+ self.location.reload();
+}
+
+function WriteMe() {
+ if ( true )
+ document.write( '<frameset cols=\"20%,*\" id=PPTHorizAdjust >' +
+ '<frame src=\"outline_collapsed.htm\" name=PPTOtl>' );
+ var distribution;
+ if ( parent.includeNotes )
+ distribution = "*,20%";
+ else
+ distribution = "*,0";
+ document.write('<frameset rows=\"' + distribution + '\" id=PPTVertAdjust >' +
+ '<frame src=' + getSlideName() + ' name=PPTSld>' +
+ '<frame src=' + getNotesName() + ' name=PPTNts>' );
+ document.write('</frameset>');
+ if ( true )
+ document.write(' </frameset>' );
+}
+
+if ( parent.msie < 0 ) {
+ self.onresize = restore;
+}
+
+WriteMe();
+//-->
+</script> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fs_navigation_bar.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fs_navigation_bar.htm
new file mode 100755
index 00000000..2b5174d1
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fs_navigation_bar.htm
@@ -0,0 +1,84 @@
+<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> <title>Navigation Bar</title>
+<script>
+<!--
+function restore() {
+if( navigator.platform != "MacPPC" )
+ self.location.reload();
+}
+ mainWin = parent.base;
+ dad = parent;
+function WriteBody()
+{
+ if( window.name != "PPTNav" ) return;
+
+ document.writeln( '<table border=0 valign=top cellpadding=0 cellspacing=0 height=100% width=100%> <tr> <td align=center valign=top> <table border=0 valign=top cellpadding=0 cellspacing=0 height=100%><tr><td align=right valign=top>' );
+ if ( dad.g_hideNav != 1 ) {
+ innerText = "";
+ if ( mainWin.GetHrefObj( mainWin.g_currentSlide ).m_origVisibility == 1 && !mainWin.g_allHidden)
+ innerText = "Slide " + mainWin.GetCurrentSlideNum() + " of " + mainWin.GetNumSlides();
+ else
+ innerText = "Hidden Slide";
+ if( dad.gIsEndShow )
+ innerText = "End of Slide Show";
+
+fEnable = dad.M_HasPrevSld();
+ if( false || fEnable )
+ {
+ prevBtn = "prev_active.gif";
+ document.write( '<a onclick="if(event) event.cancelBubble=true" href="javascript:dad.M_GoPrevSld()" >' );
+ }
+ else
+ prevBtn = "prev_disabled.gif";
+
+ document.write( '<img src="' + prevBtn + '" border=0 alt="Previous Slide" title="Previous Slide">' );
+
+var textAlign;
+ if ( false )
+ textAlign = 'top';
+ else
+ textAlign = 'center';
+
+ if( false || fEnable )
+ document.write( '</a>' );
+
+ document.write( '</td><td align=center valign=' + textAlign + '> &nbsp &nbsp <font face=\"Arial\" color=#000000 size=2>' + innerText + '</font> &nbsp &nbsp </td><td align=left valign=top>' );
+
+
+fEnable = (!dad.gIsEndShow && mainWin.EndSlideShow) || (!mainWin.EndSlideShow &&( mainWin.GetCurrentSlideNum() != mainWin.GetNumSlides() ) );
+ if( false || fEnable )
+ {
+ nextBtn = "next_active.gif";
+ document.write( '<a onclick="if(event) event.cancelBubble=true" href="javascript:dad.M_GoNextSld()" >' );
+ }
+ else
+ nextBtn = "next_disabled.gif";
+ document.write( '<img src="' + nextBtn + '" border=0 alt="Next Slide" title="Next Slide">' );
+
+ if( false || fEnable )
+ document.write( '</a>' );
+ document.write( '</td> </tr></table> </td> <td align=right valign=top>' );
+ document.write( '<a onclick="if(event) event.cancelBubble=true" href="javascript:mainWin.CloseFullScreen()" > ' );
+ document.write( '<img src="fullscrClose.gif"border=0 alt="Close" title="Close">');
+ document.write( ' </a>' );
+ }
+ document.write( '</td> </tr></table>' );
+}
+if ( mainWin.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.onmousedown = handleClick;
+}
+
+function handleClick(event) {
+ if ( event.which == 3 )
+ return false;
+ return true;
+}
+//-->
+</script>
+ </head> <body background=navbg.gif topmargin=2 onresize="restore()" scroll="no" onkeypress="parent.processNavKPH(event)" onclick="parent.processNavClick()"oncontextmenu="parent.processNavClick(); return false"> <center><script language=JavaScript><!--
+WriteBody();//-->
+</script></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fullscr.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fullscr.gif
new file mode 100755
index 00000000..85842700
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fullscr.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fullscrClose.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fullscrClose.gif
new file mode 100755
index 00000000..ccd0de13
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fullscrClose.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fullscreen.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fullscreen.htm
new file mode 100755
index 00000000..d562e618
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/fullscreen.htm
@@ -0,0 +1,48 @@
+<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 ( ! opener.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script><script language=JavaScript src=script.js></script><script language=JavaScript><!--
+var SCREEN_MODE = "FullScreen";
+ base = self;
+ g_fullscrMode = 1;LoadHTMLVersion();
+//-->
+</script> </head> <script> <!--
+closing = false;
+PPTPRESENTATION = 1;
+function getSlideName() {
+ return opener.GetHrefObj( g_currentSlide ).m_slideHref;
+}
+function initpopup() {
+ if ( base.msie < 0 )
+ NavPopup = window.open( "fs_navigation_bar.htm", "controls", "alwaysRaised=yes,WIDTH=300,HEIGHT=50");
+ else
+ NavPopup = window.open( "fs_navigation_bar.htm", "controls", "WIDTH=300,HEIGHT=50");
+ NavPopup.focus();
+}
+
+
+function WriteMe() {
+ document.write( '<frameset rows=\" *,35 \" frameborder=0> ' +
+ ' ' +
+ '<frame src=\"' + getSlideName() + '\" name=PPTSld marginheight=0 marginwidth=0 scrolling=no noresize> ' +
+ ' <frame src="fs_navigation_bar.htm" name=PPTNav marginheight=0 marginwidth=0 scrolling=no noresize> ' +
+ '</frameset>' );
+ window.focus();
+}
+
+function shutdown( ) {
+if ( ! closing )
+
+ if ( window.NavPopup && !window.NavPopup.closed )
+ window.NavPopup.close();
+}
+
+WriteMe();
+// initpopup();
+
+
+ self.onunload = shutdown;
+
+//-->
+</script> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master02.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master02.htm
new file mode 100755
index 00000000..2eebab33
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master02.htm
@@ -0,0 +1,11 @@
+<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"> <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=Robots content=NoIndex> <link rel=Stylesheet href="master03_stylesheet.css"> <script language=JavaScript src=script.js></script>
+<script>
+<!--
+ parent.location.href=document.all.item("Main-File").href
+//-->
+</script>
+ </head> <body> <div class=O style='text-align:right;position:absolute;top:.53%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black'><b>Memphis Microarray 2003</b></span></div> <div class=O style='position:absolute;top:97.52%;left:1.32%;width:42.64%; height:2.12%'><span style='color:black'><b>June 11, 2003, Rob Williams</b></span></div> <div class=O style='text-align:right;position:absolute;top:97.52%;left:58.01%; width:40.79%;height:2.12%'><span style='color:black;mso-field-code:meta16'><b>Ü#Ý</b></span><span style='color:black;mso-special-format:lastCR'><b><br> </b></span></div> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03.htm
new file mode 100755
index 00000000..89745289
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03.htm
@@ -0,0 +1,11 @@
+<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"> <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=Robots content=NoIndex> <link rel=Stylesheet href="master03_stylesheet.css"> <script language=JavaScript src=script.js></script>
+<script>
+<!--
+ parent.location.href=document.all.item("Main-File").href
+//-->
+</script>
+ </head> <body> <div style='position:absolute;top:.35%;left:6.09%;width:90.33%;height:18.19%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03_background.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03_background.png
new file mode 100755
index 00000000..abdc767d
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03_background.png
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03_stylesheet.css b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03_stylesheet.css
new file mode 100755
index 00000000..6c3dc4e2
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/master03_stylesheet.css
@@ -0,0 +1 @@
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mso-line-spacing:"-168 0 0"; mso-margin-left-alt:1449; mso-text-indent-alt:1209;} .defaultB {mso-special-format:nobullet¥;} .default {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; font-size:120%; mso-text-raise:0%; mso-line-spacing:"100 0 0"; mso-margin-left-alt:0; mso-text-indent-alt:0; mso-char-wrap:0; mso-kinsoku-overflow:0; direction:ltr; mso-word-wrap:1; mso-ansi-language:1033;} a:link {color:#009999 !important;} a:active {color:#333399 !important;} a:visited {color:#99CC00 !important;} \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/narration.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/narration.gif
new file mode 100755
index 00000000..86530132
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/narration.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/navbg.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/navbg.gif
new file mode 100755
index 00000000..de74971c
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/navbg.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/navigation_bar.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/navigation_bar.htm
new file mode 100755
index 00000000..1ea0858b
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/navigation_bar.htm
@@ -0,0 +1,91 @@
+<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>
+<script>
+<!--
+function restore() {
+if( navigator.platform != "MacPPC" )
+ self.location.reload();
+}
+
+function WriteBody()
+{
+ if( window.name != "PPTNav" ) return;
+
+ document.writeln( '<table width=\"100%\" border=0 valign=top cellpadding=0 cellspacing=0> <tr> ' );
+ drawing_app = false;
+ if ( parent.includeNotes && !false ) {
+
+ document.write( '<td align=left><a href=\"javascript:parent.ShowHideNotes()\">' +
+ ' <img src=\"notes_flag.gif\" border=0 title=\" Notes\" alt=\" Notes\">' + ' </a> </td> ' );
+
+ }
+ document.write( '<td align=center valign=top> <table border=0 valign=top cellpadding=0 cellspacing=0> <tr><td align=right>' );
+
+ innerText = "";
+ if ( parent.GetHrefObj( parent.g_currentSlide ).m_origVisibility == 1 && !parent.g_allHidden )
+ innerText = "Slide " + parent.GetCurrentSlideNum() + " of " + parent.GetNumSlides();
+ else
+ innerText = "Hidden Slide";
+
+ if ( drawing_app ) {
+ document.write( '<a href=\"javascript:parent.GoToFirst()\">' );
+ document.write( '<img src="prev_active.gif"></a> &nbsp &nbsp &nbsp &nbsp' );
+ }
+
+ fEnable = ( ( parent.g_currentSlide != 1 && parent.GetHrefObj( parent.g_currentSlide - 1 ).m_visibility == 1 ) ) ||
+ ( parent.GetCurrentSlideNum() > 1 );
+
+ if( fEnable )
+ {
+ prevBtn = "prev_active.gif";
+ document.write( '<a href=\"javascript:parent.TP_GoToPrevSld()\">' );
+ }
+ else
+ prevBtn = "prev_disabled.gif";
+
+ document.write( '<img src="' + prevBtn + '" border=0 title="Previous Slide" alt="Previous Slide" >' );
+
+ if( fEnable )
+ document.write( '</a>' );
+
+ document.write( '</td> <td align=center> ')
+ document.write( ' &nbsp &nbsp <font face=\"Arial\" color=#000000 size=2>' + innerText + '</font> &nbsp &nbsp ' );
+ document.write( '</td> <td align=left>' );
+
+ fEnable = ( parent.GetCurrentSlideNum() != parent.GetNumSlides() );
+ if( fEnable )
+ {
+ nextBtn = "next_active.gif";
+ document.write( '<a href=\"javascript:parent.TP_GoToNextSld()\">' );
+ }
+ else
+ nextBtn = "next_disabled.gif";
+
+document.write( '<img src="' + nextBtn + '" border=0 title="Next Slide" alt="Next Slide">' );
+
+ if( fEnable )
+ document.write( '</a>' );
+ if ( drawing_app ) {
+ document.write( ' &nbsp &nbsp &nbsp &nbsp<a href=\"javascript:parent.GoToLast()\">' );
+ document.write( '<img src="next_active.gif"></a>' );
+ }
+
+
+ document.write( '</td> </tr></table>' );
+
+ if ( ! drawing_app && !false ) {
+ document.write( '</td> <td align=right valign=top>' );
+ document.write( '<a href=\"javascript:parent.FullScreen()\"> ' +
+ '<img src="fullscr.gif" border=0 title="Full Screen Slide Show" alt="Full Screen Slide Show">' +
+ '</a>' );
+ }
+ document.write( '</td> </tr></table>' );
+}
+//-->
+</script>
+ </head> <body background=navbg.gif topmargin=2 scroll="no" onresize="restore()"> <center><script language=JavaScript><!--
+WriteBody();//-->
+</script></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/next_active.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/next_active.gif
new file mode 100755
index 00000000..f1677f91
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/next_active.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/next_disabled.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/next_disabled.gif
new file mode 100755
index 00000000..261df048
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/next_disabled.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/notes_flag.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/notes_flag.gif
new file mode 100755
index 00000000..cf618351
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/notes_flag.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline.gif
new file mode 100755
index 00000000..2d4aa484
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapse.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapse.gif
new file mode 100755
index 00000000..4c804d69
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapse.gif
Binary files differ
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapsed.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapsed.htm
new file mode 100755
index 00000000..5da9503b
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapsed.htm
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+</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 >&gt;</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> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>&quot;First page of data:&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>&quot;Data sources:&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>&quot;Expression estimates for App on...&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>&quot;Critiquing the App data the...&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>&quot;App expression after windsorizing&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>&quot;Discovering shared expression patterns&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>&quot;Transcript neighborhoods&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>&quot;App and Atcay transcript scatterplot&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>&quot;App transcript and eight of...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p15" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('15')" id=AREF>&quot;Correlations of App with classical...&quot;</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 >&gt;</ilayer>'); 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+</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 >&gt;</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> </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 study expression variation and covariation (slides 2&#8211;16)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators (slides 17&#8211;30)</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >&gt;</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 >&gt;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>&quot;First page of data:&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>&quot;Data sources:&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>&quot;Expression estimates for App on...&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>&quot;Critiquing the App data the...&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>&quot;App expression after windsorizing&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>&quot;Discovering shared expression patterns&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>&quot;Transcript neighborhoods&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>&quot;App and Atcay transcript scatterplot&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>&quot;App transcript and eight of...&quot;</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 >&gt;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p15" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('15')" id=AREF>&quot;Correlations of App with classical...&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p16" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('16')" id=AREF>&quot;Network Graph of App with...&quot;</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 >&gt;</ilayer>'); } </script></td> <td width=100% id="p17" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('17')" id=AREF>&quot;Summary of Part 1:&quot;</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 >&gt;</ilayer>'); 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+ if( fTrans )
+ SlideObj.filters.revealtrans.Play()
+}
+function MakeNotesVis()
+{
+ if( !IsNts() ) return false
+ SlideObj.style.display="none"
+ nObj = document.all.item("NotesObj")
+ parent.SetHasNts(0)
+ if( nObj ) {
+ nObj.style.display=""
+ parent.SetHasNts(1)
+ }
+ return 1
+}
+function Redirect( frmId,sId )
+{
+ var str=document.location.hash,idx=str.indexOf('#')
+ if(idx>=0) str=str.substr(1);
+ if( window.name != frmId && ( sId != str) ) {
+ obj = document.all.item("Main-File")
+ window.location.href=obj.href+"#"+sId
+ return 1
+ }
+ return 0
+}
+function HideMenu() { if( frames["PPTSld"] && PPTSld.document.all.item("ctxtmenu") && PPTSld.ctxtmenu.style.display!="none" ) { PPTSld.ctxtmenu.style.display='none'; return true } return false }
+function IsWin( name ) { return window.name == name }
+function IsNts() { return IsWin("PPTNts") }
+function IsSldOrNts() { return( IsWin("PPTSld")||IsWin("PPTNts") ) }
+function SupportsPPTAnimation() { return( navigator.platform == "Win32" && navigator.appVersion.indexOf("Windows")>0 ) }
+function SupportsPPTHTML()
+{
+ var appVer=navigator.appVersion, msie=appVer.indexOf( "MSIE " ), inex = appVer.indexOf( "Internet Explorer " ), ver=0
+ if( msie >= 0 )
+ ver=parseFloat( appVer.substring( msie+5, appVer.indexOf(";",msie) ) )
+ else if( inex >= 0 )
+ ver=parseFloat( appVer.substring( inex+18, appVer.indexOf(";",inex) ) )
+ else
+ ver=parseInt(appVer)
+
+ return( ver >= 4 )
+}
+var MHTMLPrefix = CalculateMHTMLPrefix();
+function CalculateMHTMLPrefix()
+{
+ if ( document.location.protocol == 'mhtml:') {
+ href=new String(document.location.href)
+ Start=href.indexOf('!')+1
+ End=href.lastIndexOf('/')+1
+ if (End < Start)
+ return href.substring(0, Start)
+ else
+ return href.substring(0, End)
+ }
+ return '';
+}
+
+function LoadNavSld(slideId) {
+playList();
+parent.createCM();
+ if( !g_supportsPPTHTML ) return
+ if( IsWin("PPTSld") && slideId )
+ parent.base.SldUpdated(slideId)
+ self.focus();
+
+}
+var hasNarration = false;
+function _RSW()
+{
+ if( !g_supportsPPTHTML || IsNts() ||
+ ( !g_scaleInFrame && (( window.name != "PPTSld" ) ) ) )
+ return
+
+ cltWidth=document.body.clientWidth
+ cltHeight=document.body.clientHeight
+ factor=(1.0*cltWidth)/g_origW
+ if( cltHeight < g_origH*factor )
+ factor=(1.0*cltHeight)/g_origH
+
+ newSize = g_origSz * factor
+ if( newSize < 1 ) newSize=1
+
+ s=SlideObj.style
+ s.fontSize=newSize+"px"
+ s.posWidth=g_origW*factor
+ s.posHeight=g_origH*factor
+ s.posLeft=(cltWidth-s.posWidth)/2
+ s.posTop=(cltHeight-s.posHeight)/2
+
+ if ( hasNarration ) {
+ obj = document.all.NSPlay.style;
+ mySld = document.all.SlideObj.style;
+ obj.position = 'absolute';
+ obj.posTop = mySld.posTop + mySld.posHeight - 20;
+ obj.posLeft = mySld.posLeft + mySld.posWidth - 20;
+ }
+ if( g_scaleHyperlinks )
+ ScaleHyperlinks( factor );
+}
+function IsMac() {
+ return (window.navigator.platform.indexOf("Mac") >= 0 );
+}
+
+function HitOK( evt ) {
+ //Nav Only function
+ return (evt.which == 1 || (IsMac() && evt.which == 3) );
+}
+function _KPH(event)
+{
+
+ if ( parent.base.msie < 0 ) {
+
+ if ( ( (event.target.name && event.target.name == "hasMap" ) || (event.target.href && event.target.href != "") ) && parent.g_docTable[0].type != "jpeg" && HitOK( event ) ) {
+ return; /* to make hyperlinks in fullscreen mode traversable */
+ }
+ if( IsContextMenu() )
+ return parent.KPH(event);
+ if ( parent.IsFullScrMode() && event.which == 27 )
+ parent.base.CloseFullScreen();
+ else if ( parent.base.IsFullScrMode() && ( (!IsMac() && event.which == 3) || ( IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) )
+ return parent.KPH(event);
+ 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( " > &nbsp " + 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;
+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 );
+ ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF );
+ }
+}
+
+function hrefList( slideHref, notesHref, visible, slideIdx, type )
+{
+ this.m_slideHref = slideHref;
+ this.m_notesHref = notesHref;
+ this.m_navbarHref = NAVBAR_HREF;
+ this.m_origVisibility = visible;
+ this.m_visibility = visible;
+ this.m_slideIdx = slideIdx;
+ this.type = type;
+}
+
+function IsFullScrMode() {
+ return g_fullscrMode;
+}
+
+
+function IsFramesMode() {
+ return (1 - g_fullscrMode);
+}
+
+function SldUpdated( id )
+{
+ if ( ( id != GetHrefObj( g_currentSlide ).m_slideHref ) || ( g_currentSlide == g_lastVisibleSld ) ){
+ g_prevSlide = g_currentSlide;
+ g_currentSlide = GetSlideNum( id );
+ obj = GetHrefObj( g_currentSlide );
+ if( !SIMPLE_FRAMESET )
+ ChangeFrame( NOTES_FRAME, obj.m_notesHref );
+ ChangeFrame( NAVBAR_FRAME, NAVBAR_HREF );
+ }
+}
+
+function ToggleOutline() {
+ g_showoutline = 1 - g_showoutline;
+ writeMyFrame();
+}
+
+function ShowHideNotes() {
+ g_shownotes = 1 - g_shownotes;
+ writeMyFrame();
+}
+
+function writeMyFrame() {
+ SetFSMode(0);
+ obj = frames[MAIN_FRAME];
+
+ var curslide = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_slideHref;
+ var curnotes = g_baseURL + "/" + GetHrefObj( g_currentSlide ).m_notesHref;
+ var otlhref = g_baseURL + "/" + g_outline_href;
+ if ( msie < 0 ) {
+ if ( ! g_showoutline && g_shownotes ) {
+ obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \
+ <frameset rows=\"*,20%\" id=\"frameset2\" > \
+ <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \
+ <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \
+ </frameset> </html>' );
+ }
+ else if( g_showoutline && g_shownotes ){
+ obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \
+ <frameset cols=\"20%,*\" id=\"frameset1\"> \
+ <frame src=\"' + otlhref + '\" name=PPTOtl> \
+ <frameset rows=\"*,20%\" id=\"frameset2\" > \
+ <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \
+ <frame src=\"' + curnotes + '\" name=PPTNts marginheight=0 marginwidth=0> \
+ </frameset> </frameset></html>' );
+ }
+ else if ( !g_shownotes && !g_showoutline ) {
+ obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \
+ <frameset rows="*,0" frameborder=0 > \
+ <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \
+ </frameset> </html>' );
+ }
+ else if( !g_shownotes && g_showoutline ) {
+ obj.document.write( '<HTML><HEAD><SCRIPT language=JavaScript src=' + g_baseURL + '/script.js></SCRIPT><SCRIPT> base = parent; <\/SCRIPT><\/HEAD> \
+ <frameset cols=\"20%,*\" id=\"frameset1\"> \
+ <frame src=\"' + otlhref + '\" name=PPTOtl> \
+ <frame src=\"' + curslide + '\" name=PPTSld marginheight=0 marginwidth=0> \
+ </frameset></html>' );
+ }
+ obj.document.close();
+ }
+ else {
+ if ( g_showoutline ) {
+ obj.PPTHorizAdjust.cols = "20%,*";
+ obj.PPTOtl.location.reload();
+ }
+ else {
+ obj.PPTHorizAdjust.cols = "0,*";
+ }
+ if ( g_shownotes ) {
+ obj.PPTVertAdjust.rows = "*,20%";
+ obj.PPTNts.location.href = curnotes;
+ }
+ else {
+ obj.PPTVertAdjust.rows = "*,0";
+ }
+ }
+ ChangeFrame( OUTLINE_NAVBAR_FRAME, OUTLINE_NAVBAR_HREF );
+}
+
+function FullScreen() {
+ g_done = 0;
+
+
+ SetFSMode(1);
+ if ( msie >= 0 )
+ FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", null, "fullscreen=yes");
+ else {
+ var height = screen.availHeight;
+ if ( window.navigator.platform.indexOf( "Mac" ) >= 0 ) {
+ height -= 30;
+ }
+ FSWin = window.open( g_baseURL + "/" + "fullscreen.htm", "null", "height="+ height + ",width=" + screen.availWidth + ",screenX=0,screenY=0");
+ }
+}
+
+function SetFSMode( i ) {
+
+}
+
+function Slide( i ) {
+ SetFSMode(0);
+ GoToSld(GetHrefObj(i).m_slideHref);
+}
+
+function TP_GoToNextSld() {
+ SetFSMode(0);
+ GoToNextSld();
+}
+
+function TP_GoToPrevSld() {
+ SetFSMode(0);
+ GoToPrevSld();
+}
+
+function CloseFullScreen() {
+ g_done = 0;
+
+ if ( IsNav() ){
+ if ( self.opener )
+ opener.FSWin = null;
+ }
+ window.close();
+}
+
+function slidenum(i) {
+ var slidename = "slide";
+ if ( i < 10 )
+ return ( slidename + "000" + i);
+ else if ( i < 100 )
+ return ( slidename + "00" + i );
+ else if ( i < 1000 )
+ return (slidename + "0" + i );
+ else
+ return (slidename + i );
+}
+function UpdateLastVisibleSlide( index ) {
+ if ( g_lastVisibleSld < index )
+ g_lastVisibleSld = index;
+}
+
+function jpegArray( numSlides ) {
+count_hidden = 0;
+ g_docTable = new Array();
+ for( i=0; i<numSlides; i++ ) {
+ j = 2 * 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, "jpeg" );
+ else
+ g_docTable[i] = new hrefList( str, BLANK_NOTES_HREF, g_hiddenSlide[i], i+1-count_hidden, "jpeg" );
+ if ( !g_hiddenSlide[i] ) count_hidden++;
+ else UpdateLastVisibleSlide( i+1 );
+ }
+}
+
+function ieArray( numSlides ) {
+count_hidden = 0;
+ g_docTable = new Array();
+ for( i=0; i<numSlides; i++ ) {
+ var str = slidenum(i+1) +".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, "ie" );
+ 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() )
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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
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+if( !IsSldOrNts() ) return;
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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:.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&#8211;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&#8211;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
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new file mode 100755
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+<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
new file mode 100755
index 00000000..8627e129
--- /dev/null
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+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">&nbsp; </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">&nbsp; </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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp; </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
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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
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm
@@ -0,0 +1,5 @@
+<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">&nbsp; </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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp; </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
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+if ( ! top.PPTPRESENTATION ) {
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+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.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
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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
new file mode 100755
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm
@@ -0,0 +1,5 @@
+<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
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@@ -0,0 +1,25 @@
+<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> <!--.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"
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+ 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">&nbsp; </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">&nbsp; </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
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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
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+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm
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+<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">&nbsp; </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">&nbsp; </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
new file mode 100755
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+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
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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
new file mode 100755
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm
@@ -0,0 +1,5 @@
+<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
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new file mode 100755
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+<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
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new file mode 100755
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm
@@ -0,0 +1,5 @@
+<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
new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+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">&nbsp;&nbsp; </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
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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
new file mode 100755
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_notes_pane.htm
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+<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
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+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><!--
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+var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1;
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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%'> <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
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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
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+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm
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+<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
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+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="slide0009.htm"
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+ 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: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
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+<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" );
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+</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
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+gId="slide0010.htm"
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+if( !IsNts() ) Redirect( "PPTSld", gId );
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+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: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
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+<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
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+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="slide0011.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: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
new file mode 100755
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new file mode 100755
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm
@@ -0,0 +1,5 @@
+<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
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+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="slide0012.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: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
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new file mode 100755
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_notes_pane.htm
@@ -0,0 +1,5 @@
+<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
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new file mode 100755
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+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="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;
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+</script><script for=window event=onload language=JavaScript><!--
+if( !IsSldOrNts() ) return;
+if( MakeNotesVis() ) return;
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+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
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new file mode 100755
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm
@@ -0,0 +1,5 @@
+<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
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content="Aug-15-05: App transcript coexpression neighborhood"> <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="slide0014.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: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">&nbsp; </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
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new file mode 100755
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm
@@ -0,0 +1,5 @@
+<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">&nbsp; </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
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+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="slide0015.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: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
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--- /dev/null
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@@ -0,0 +1,5 @@
+<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
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+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="slide0016.htm"
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+ parent.base.g_done = 1;
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+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 );
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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><!--
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+<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>
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+</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
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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: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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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">&nbsp;</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> <script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018.htm
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+if( !IsSldOrNts() ) return;
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+LoadSld( gId );
+playList();MakeSldVis(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: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'> <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><!--
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+</script> <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> </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>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> </layer> <script language=JavaScript><!--
+//-->
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+
+}
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new file mode 100755
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--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019_notes_pane.htm
@@ -0,0 +1,5 @@
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new file mode 100755
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+ 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> <div><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>Enter<br> </span></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div style='mso-line-spacing:"-224 0 0"'><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> </layer></div> </layer></div> </layer><script>
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+ 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 = 0.11 * 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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+</script> <div><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div> <layer> <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%; mso-text-raise:0%'></div> </layer> <layer> <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%; mso-text-raise:0%'></div> </layer> <layer> <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%; mso-text-raise:0%'></div> </layer> <layer> <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%; mso-text-raise:0%'></div> </layer> <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>
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+ 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 + ' >' );
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+</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>
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+</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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>and type</span></span></layer></div> </layer></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ht = 0.13 * g_height;
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+'<img border=0 src="slide0002_image004.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>Please link to the web site:<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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">&nbsp;&nbsp; </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">&nbsp; </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> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0021.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0021.htm
new file mode 100755
index 00000000..0e0eb529
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+</script></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.38 * g_width;
+yy = 0.49 * g_height;
+ht = 0.48 * g_height;
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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>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> </layer> <script language=JavaScript><!--
+//-->
+</script><script language=JavaScript><!--
+function playList() {
+
+}
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diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0022.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0022.htm
new file mode 100755
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+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0022.htm
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+if ( ! top.PPTPRESENTATION ) {
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+}
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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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>RESULTS OF THE APP SEARCH.<span style="mso-spacerun: yes">&nbsp; </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">&nbsp; </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><!--
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+
+}
+//-->
+</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
new file mode 100755
index 00000000..10a6218a
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm
@@ -0,0 +1,128 @@
+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
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+ 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: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'>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> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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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>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() {
+
+}
+//-->
+</script> </body> </html> \ 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
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--- /dev/null
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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
new file mode 100755
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+}
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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
new file mode 100755
index 00000000..7dac49e1
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+</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script>
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+</script><span 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>
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+</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>
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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>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> </layer> <script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0028.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0028.htm
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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>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> <script language=JavaScript><!--
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diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0029.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0029.htm
new file mode 100755
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+ 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: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'>Transcript neighborhoods</span></div> </layer></div> </layer><script>
+ mytop = 0.07 * g_height; myleft = 0.02 * g_width; myheight = 0.91 * g_height; mywidth = 0.85 * 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=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><!--
+function playList() {
+
+}
+//-->
+</script> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0030.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0030.htm
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+ 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 = 0.9 * 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: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> </layer></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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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>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><!--
+//-->
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+}
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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
new file mode 100755
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+ht = g_height;
+wd = g_width;
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+ mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.14 * 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 = 0.96 * 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: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'> transcript and eight of its neighbors</span></div> </layer></div> </layer><script>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
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+yy = 0.09 * g_height;
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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>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
new file mode 100755
index 00000000..85ee47fe
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@@ -0,0 +1,118 @@
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+ LoadNavSld("slide0032.htm");
+}//-->
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+ mytop = 0.82 * g_height; myleft = 0.04 * g_width; myheight = 0.18 * g_height; mywidth = 0.96 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div></div> </layer><script>
+ mytop = -0.02 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 1.05 * 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 = 0.07 * g_height; mywidth = 1.04 * 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%'><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> </layer></div> </layer><script>
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+'<img border=0 src="slide0014_image031.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0.1 * g_height; myleft = 0.81 * g_width; myheight = 0.09 * g_height; mywidth = 0.18 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.81 * g_width;
+yy = 0.1 * g_height;
+ht = 0.09 * g_height;
+wd = 0.18 * g_width;
+document.write(
+'<img border=0 src="slide0014_image033.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>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">&nbsp; </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
new file mode 100755
index 00000000..042ca4ad
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm
@@ -0,0 +1,104 @@
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <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>
+function font_size() {
+ var min = window.innerWidth/20;
+ if ( min > window.innerHeight/20 )
+ min = window.innerHeight/20;
+
+ return min+"pt";
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+function restore() {
+ self.location.reload();
+}
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+ document.SlideLayer.width = window.innerWidth;
+ document.SlideLayer.height = window.innerHeight;
+}
+document.captureEvents(Event.MOUSEDOWN);
+document.captureEvents(Event.KEYPRESS);
+document.onkeypress = _KPH ;
+document.onmousedown = _KPH ;
+ parent.base.highlite();
+</script><script language=JavaScript><!--
+function DoOnLoad() {
+ LoadNavSld("slide0033.htm");
+}//-->
+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script>
+
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+document.SlideLayer.clip.top = 0;
+document.SlideLayer.clip.left = 0;
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+</script> <div><script language=JavaScript><!--
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+wd = g_width;
+document.write(
+'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </layer><script>
+ mytop = 0 * g_height; myleft = 0 * 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'>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> </layer><script>
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+</script> <div><script language=JavaScript><!--
+xx = 0.04 * g_width;
+yy = 0.28 * g_height;
+ht = 0.7 * g_height;
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+document.write(
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+//-->
+</script></div> </layer><script>
+ mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.19 * g_height; mywidth = 0.33 * g_width;
+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script> <div><script language=JavaScript><!--
+xx = 0.04 * g_width;
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+ht = 0.19 * g_height;
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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
new file mode 100755
index 00000000..3cf1ac70
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0034.htm
@@ -0,0 +1,93 @@
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <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>
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+document.captureEvents(Event.MOUSEDOWN);
+document.captureEvents(Event.KEYPRESS);
+document.onkeypress = _KPH ;
+document.onmousedown = _KPH ;
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+ LoadNavSld("slide0034.htm");
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+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script>
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+</script> <div><script language=JavaScript><!--
+ht = g_height;
+wd = g_width;
+document.write(
+'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' );
+//-->
+</script></div> </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><!--
+//-->
+</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/slide0035.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0035.htm
new file mode 100755
index 00000000..ca5ac8bb
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0035.htm
@@ -0,0 +1,151 @@
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+<script language=JavaScript>
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+document.onkeypress = _KPH ;
+document.onmousedown = _KPH ;
+ parent.base.highlite();
+</script><script language=JavaScript><!--
+function DoOnLoad() {
+ LoadNavSld("slide0035.htm");
+}//-->
+</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script>
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+document.SlideLayer.clip.left = 0;
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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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+ 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>
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+</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">&nbsp;</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">&nbsp;</span>You know some methods to check data quality<br> </span></span></layer></div> </layer><script>
+ mytop = 0.1 * 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'>3.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes">&nbsp;</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">&nbsp;</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">&nbsp;</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: 144;mso-margin-left-alt:144'><script>
+ mytop = 0 * 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 + ' >' );
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+ 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">&nbsp;</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%; color:#E9EB5D;mso-color-index:3'>disequilibrium. Finally, it can be due to 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%; color:#E9EB5D;mso-color-index:3'>correlations. Test and be skeptical.</span></span></layer></div> </layer></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/slide0036.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0036.htm
new file mode 100755
index 00000000..ccec2e7d
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0036.htm
@@ -0,0 +1,112 @@
+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
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+wd = g_width;
+document.write(
+'<img src="master03_background.png" height=' + ht + ' width=' + wd + '>' );
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+</script></div> </layer><script>
+ mytop = 0.02 * g_height; myleft = 0.02 * g_width; myheight = 0.09 * g_height; mywidth = 0.94 * 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 = 0.06 * 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:"-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> </layer><script>
+ mytop = 0.16 * g_height; myleft = 0.06 * g_width; myheight = 0.24 * g_height; mywidth = 0.9 * g_width;
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+</script> <div><script>
+ mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.24 * g_height; mywidth = 0.87 * g_width;
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+</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;
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+ 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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
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+ mytop = 0.83 * g_height; myleft = 0.04 * g_width; myheight = 0.15 * 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%'><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>
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+ document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' );
+</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and R. Clark (July 15, </span></span></layer><script>
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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>END</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/slide0037.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0037.htm
new file mode 100755
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+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
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+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0037.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0001.gif border=0 usemap="#Slide0001.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0038.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0038.htm
new file mode 100755
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+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0038.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0002.gif border=0 usemap="#Slide0002.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0039.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0039.htm
new file mode 100755
index 00000000..933dd079
--- /dev/null
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+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0039.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0003.gif border=0 usemap="#Slide0003.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0040.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0040.htm
new file mode 100755
index 00000000..d259ab62
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0040.htm
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+<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 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"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0040.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0004.gif border=0 usemap="#Slide0004.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0041.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0041.htm
new file mode 100755
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--- /dev/null
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+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0041.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0005.gif border=0 usemap="#Slide0005.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0042.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0042.htm
new file mode 100755
index 00000000..f0673f6c
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0042.htm
@@ -0,0 +1,34 @@
+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0042.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0006.gif border=0 usemap="#Slide0006.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0043.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0043.htm
new file mode 100755
index 00000000..67760c34
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0043.htm
@@ -0,0 +1,34 @@
+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0043.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0007.gif border=0 usemap="#Slide0007.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0044.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0044.htm
new file mode 100755
index 00000000..6c7be85e
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0044.htm
@@ -0,0 +1,34 @@
+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0044.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0008.gif border=0 usemap="#Slide0008.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0045.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0045.htm
new file mode 100755
index 00000000..19a153ed
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0045.htm
@@ -0,0 +1,34 @@
+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0045.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0009.gif border=0 usemap="#Slide0009.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0046.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0046.htm
new file mode 100755
index 00000000..e210d3d5
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0046.htm
@@ -0,0 +1,34 @@
+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0046.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0010.gif border=0 usemap="#Slide0010.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0047.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0047.htm
new file mode 100755
index 00000000..c2de15b1
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0047.htm
@@ -0,0 +1,34 @@
+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
+ window.location.replace( "endshow.htm" );
+}
+</script> <meta name=Description content=Aug-15-05> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:80% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript>
+ if ( parent.base.msie < 0 ) {
+ document.captureEvents(Event.MOUSEDOWN);
+ document.captureEvents(Event.KEYPRESS);
+ document.onkeypress = _KPH;
+ document.onmousedown = _KPH;
+ }
+
+function restore() {
+ if ( parent.base.msie < 0 )
+ self.location.reload();
+}
+</script>
+<script language=JavaScript>
+function flatLoad() {
+if ( !parent.IsFullScrMode() )
+ parent.base.highlite();
+DoOnLoad();
+
+
+ if ( parent.IsFullScrMode() && parent.NavPopup && !parent.NavPopup.closed )
+ parent.NavPopup.focus();
+ else
+ self.focus();
+ parent.base.SldUpdated( "slide0047.htm" );
+ }
+ </script><script language=JavaScript><!--
+function DoOnLoad() {
+ }//-->
+</script> </head> <body bgcolor="#000000" onresize="restore()" onload="flatLoad()" onclick="DocumentOnClick(event)" onkeypress="_KPH(event)"> <center><img src=Slide0011.gif border=0 usemap="#Slide0011.gif_map"></center> </body> </html> \ No newline at end of file
diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0048.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0048.htm
new file mode 100755
index 00000000..808d5c5c
--- /dev/null
+++ b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0048.htm
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+<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 href="webqtl_demo2_part1.ppt.ppt"> <script>
+if ( ! top.PPTPRESENTATION ) {
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<HTML><HEAD><TITLE>Powerpoint / GeneNetwork</TITLE>
+<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
+<base href="http://www.genenetwork.org/">
+<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'>
+<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'>
+<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>
+</HEAD>
+<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff>
+<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0>
+ <TBODY>
+ <TR>
+ <script language="JavaScript" src="/javascript/header.js"></script>
+ </TR>
+ <TR>
+ <TD bgColor=#eeeeee class="solidBorder">
+ <Table width= "100%" cellSpacing=0 cellPadding=5><TR>
+ <!-- Body Start from Here -->
+ <TD vAlign=top width="100%" height=200 bgColor=#eeeeee>
+ <P class="title">GeneNetwork PowerPoint Demonstrations <A HREF="/webqtl/WebQTL.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P>
+ <blockquote>
+ <P class="subtitle">GeneNetwork Demonstration Part I </P>
+
+<P>Part I: A short introduction on <B>how to exploit GeneNetwork to explore variation and covariation among traits</B>. This 18-slide PowerPoint side show uses the beta amyloid precursor as an example.
+
+ <blockquote>
+ <UL>
+ <LI>View in <A Href="/tutorial/ppt/html/webqtl_demo2_part1.ppt.htm" class="normalsize">HTML</a>
+ <LI>Download <A Href="/tutorial/ppt/ppt/webqtl_demo2_part1.ppt" class="normalsize">Powerpoint</a> file
+ </UL>
+ </blockquote>
+ <P class="subtitle">WebQTL Demonstration Part II </P>
+
+<P>Part II: <B>A continutation that explains <B>how to map chromosomal locations (QTLs) that modulate variation in quantitative traits using the WebQTL mapping module of the GeneNetwork.</B>
+
+
+
+ <blockquote>
+ <UL>
+ <LI>View in <A Href="/tutorial/ppt/html/webqtl_demo2.ppt.htm" class="normalsize">HTML</a>
+ <LI>Download <A Href="/tutorial/ppt/ppt/webqtl_demo2.ppt" class="normalsize">Powerpoint</a> file
+ </UL>
+
+ </blockquote>
+
+
+<P>
+<P>Files last updated by RWW, July 23, 2005.
+
+
+
+
+ </blockquote>
+ </TD>
+ </TR></TABLE>
+ </TD>
+ </TR>
+ <TR>
+ <TD align=center bgColor=#ddddff class="solidBorder">
+ <TABLE width="90%">
+ <script language='JavaScript' src='/javascript/footer.js'></script>
+ </TABLE>
+ </TD>
+ </TR>
+</TABLE>
+<!-- /Footer -->
+<!-- menu script itself. you should not modify this file -->
+<script language="JavaScript" src="/javascript/menu_new.js"></script>
+<!-- items structure. menu hierarchy and links are stored there -->
+<script language="JavaScript" src="/javascript/menu_items.js"></script>
+<!-- files with geometry and styles structures -->
+<script language="JavaScript" src="/javascript/menu_tpl.js"></script>
+<script language="JavaScript">
+ <!--//
+ // Note where menu initialization block is located in HTML document.
+ // Don't try to position menu locating menu initialization block in
+ // some table cell or other HTML element. Always put it before </body>
+ // each menu gets two parameters (see demo files)
+ // 1. items structure
+ // 2. geometry structure
+ new menu (MENU_ITEMS, MENU_POS);
+ // make sure files containing definitions for these variables are linked to the document
+ // if you got some javascript error like "MENU_POS is not defined", then you've made syntax
+ // error in menu_tpl.js file or that file isn't linked properly.
+
+ // also take a look at stylesheets loaded in header in order to set styles
+ //-->
+</script>
+</BODY>
+</HTML>
diff --git a/web/tutorial/ppt/ppt/webqtl_demo2.ppt b/web/tutorial/ppt/ppt/webqtl_demo2.ppt
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diff --git a/web/tutorial/ppt/ppt/webqtl_demo2_part1.ppt b/web/tutorial/ppt/ppt/webqtl_demo2_part1.ppt
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