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b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master02.htm deleted file mode 100755 index b696e328..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/master02.htm +++ /dev/null @@ -1,11 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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%; 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document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes"> </span><br> link to www.genenetwork.org</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>Slide 2</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Slide 3</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF><font face=Verdana>Discovering upstream modulatory loci</font></a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>WebQTL searches for upstream controllers</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>Genetic versus Physical maps for App expression</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>Physical map for distal chromosome 7</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>Evaluating candidate genes</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>Physical maps are zoomable</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>Evaluating Ctbp2 as a candidate QTL for App</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>Evaluating Ctbp2 using other resources</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"Summary of Part 2"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>Test Questions</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expand.gif b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expand.gif deleted file mode 100755 index c8c72b13..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expand.gif +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expanded.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expanded.htm deleted file mode 100755 index c33cf334..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_expanded.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 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> <style> <!--a {text-decoration: none;}--> </style> </head> <body bgcolor=black text=white link=white vlink=white alink=white onload=" parent.base.highlite();" onresize="self.location.reload();"> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes"> </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 2–17)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators (slides 18–29)</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>Slide 2</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Slide 3</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF><font face=Verdana>Discovering upstream modulatory loci</font></a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>WebQTL searches for upstream controllers</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>Genetic versus Physical maps for App expression</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>Physical map for distal chromosome 7</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>Evaluating candidate genes</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>Physical maps are zoomable</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>Evaluating Ctbp2 as a candidate QTL for App</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>Evaluating Ctbp2 using other resources</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"Summary of Part 2"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Summary of Part 2</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>Test Questions</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_navigation_bar.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_navigation_bar.htm deleted file mode 100755 index 85b11c52..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/outline_navigation_bar.htm +++ /dev/null @@ -1,37 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); 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-} - -function DocumentOnClick(event) -{ - if ( g_doAdvOnClick && !parent.IsFullScrMode() ) { - parent.base.TP_GoToNextSld(); - return; - } - - if ( parent.base.msie < 0 ) - { - if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || - (event && ( (event.which == 32) || (event.which == 13) ) ) ) - parent.M_GoNextSld(); - return; - } - if( IsNts() || (parent.IsFullScrMode() && parent.HideMenu() ) ) return; - if( ( g_allowAdvOnClick && parent.IsFullScrMode() ) || g_doAdvOnClick || - (event && ( (event.keyCode==32) || (event.keyCode == 13) ) ) ) - parent.M_GoNextSld(); -} - - -var g_supportsPPTHTML = SupportsPPTHTML(), g_scaleInFrame = true, gId="", g_bgSound="", - g_scaleHyperlinks = false, g_allowAdvOnClick = true, g_showInBrowser = false, g_doAdvOnClick = false; - - var g_showAnimation = 0; -var g_hasTrans = false, g_autoTrans = false, g_transSecs = 0; -var g_animManager = null; - -var ENDSHOW_MESG="End of slide show, click to exit.", SCREEN_MODE="Frames", gIsEndShow=0, NUM_VIS_SLDS=14, SCRIPT_HREF="script.js", FULLSCR_HREF="fullscreen.htm"; -var gCurSld = gPrevSld = 1, g_offset = 0, gNtsOpen = gHasNts = gOtlTxtExp = gNarrationPaused = false, gOtlOpen = true -window.gPPTHTML=SupportsPPTHTML() -var g_hideNav = 0; -function UpdNtsPane(){ PPTNts.location.replace( MHTMLPrefix+GetHrefObj( gCurSld ).mNtsHref ) } -function UpdNavPane( sldIndex ){ if(gNavLoaded) PPTNav.UpdNav() } -function UpdOtNavPane(){ if(gOtlNavLoaded) PPTOtlNav.UpdOtlNav() } -function UpdOtlPane(){ if(gOtlLoaded) PPTOtl.UpdOtl() } -function SetHasNts( fVal ) -{ - if( gHasNts != fVal ) { - gHasNts=fVal - UpdNavPane() - } -} - -function ToggleVNarration() -{ - if ( base.msie < 0 ) { - PPTSld.ToggleSound( false, PPTSld.document.NSPlay ); - return; - } - - rObj=PPTSld.document.all("NSPlay") - if( rObj ) { - if( gNarrationPaused ) - rObj.Play() - else - rObj.Pause() - - gNarrationPaused=!gNarrationPaused - } -} - -function PrevSldViewed(){ GoToSld( GetHrefObj(gPrevSld).mSldHref ) } -function HasPrevSld() { return ( gIsEndShow || ( g_currentSlide != 1 && GetHrefObj( g_currentSlide-1 ).mVis == 1 )||( GetCurrentSlideNum() > 1 ) ) } -function HasNextSld() { return (GetCurrentSlideNum() != GetNumSlides()) } -function StartEndShow() -{ -// g_hideNav = 1; -// PPTNav.location.reload(); - if( PPTSld.event ) PPTSld.event.cancelBubble=true - - doc=PPTSld.document - doc.open() - doc.writeln('<html><head><script > /*defer>*/ g_ctxmenu = 0; ' + - 'if( parent.base.msie < 0 ) { document.captureEvents(Event.KEYPRESS); document.captureEvents(Event.MOUSEDOWN); document.onkeypress = _KPH; document.onmousedown = _KPH; } ' + - 'function DocumentOnClick(event) { return _KPH(event); } function IsContextMenu() { return (g_ctxmenu ==1); } ' + - 'function _KPH(event)' + - '{ ' + - 'if ( parent.base.msie < 0 && (parent.IsFullScrMode() ) && event ) { if ( (!parent.IsMac() && event.which == 3) || ( parent.IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { return parent.KPH(event); } ' + - ' else if (event.which == 27 || event.which == 32 || event.which == 13 || parent.HitOK( event ) || (event.which == 78) || (event.which == 110) || (event.which == 29) || (event.which == 31) || (event.which == 12) ) { if ( IsContextMenu() ) { return parent.KPH(event); } parent.base.CloseFullScreen(); return; } ' + - ' else if ( (event.which == 80) || (event.which == 112) || (event.which == 30) || (event.which == 28) || (event.which == 11) || (event.which == 8) ) { parent.M_GoPrevSld(); } } ' + - 'if( parent.HideMenu() ) return; if( (parent.IsFullScrMode() ) && event) { if ( (event.keyCode==27 || event.keyCode == 13 || event.keyCode==32 || event.type=="click" ) || (event.keyCode == 78) || (event.keyCode == 110) ) { parent.base.CloseFullScreen(); }' + - ' else if ( (event.keyCode == 80) || (event.keyCode == 112) ) { parent.M_GoPrevSld(); } } } function Unload() { parent.gIsEndShow=0; } function SetupEndShow() { if ( !parent.IsFullScrMode() ) { return; } else { parent.PPTNav.location.reload(); } parent.gIsEndShow=1; if ( parent.g_docTable[0].type != "jpeg" ) { if ( parent.base.msie < 0 ) {parent.createCM(); } document.oncontextmenu=parent._CM; } }</script></head><body scroll=\"no\" onclick=\"DocumentOnClick(event)\" onkeypress=\"_KPH(event)\" bgcolor=\"black\" onload=\"SetupEndShow()\" onunload=\"Unload()\"><center><p><font face=Tahoma color=white size=2><br><b>' + ENDSHOW_MESG + '</b></font></p></center></body></html>') - doc.close() -} -function SetSldVisited(){ gDocTable[gCurSld-1].mVisited=true } -function IsSldVisited(){ return gDocTable[gCurSld-1].mVisited } -function hrefList( sldHref, visible, sldIdx ) -{ - this.mSldHref= this.mNtsHref = sldHref - this.mSldIdx = sldIdx - this.mOrigVis= this.mVis = visible - this.mVisited= false -} -var gDocTable = new Array( - new hrefList("slide0001.htm", 1, 1), - new hrefList("slide0002.htm", 1, 2), - new hrefList("slide0003.htm", 1, 3), - new hrefList("slide0004.htm", 1, 4), - new hrefList("slide0005.htm", 1, 5), - new hrefList("slide0006.htm", 1, 6), - new hrefList("slide0007.htm", 1, 7), - new hrefList("slide0008.htm", 1, 8), - new hrefList("slide0009.htm", 1, 9), - new hrefList("slide0010.htm", 1, 10), - new hrefList("slide0011.htm", 1, 11), - new hrefList("slide0012.htm", 1, 12), - new hrefList("slide0013.htm", 1, 13), - new hrefList("slide0014.htm", 1, 14) -); - -function ImgBtn( oId,bId,w,action ) -{ - var t=this - t.Perform = _IBP - t.SetActive = _IBSetA - t.SetInactive= _IBSetI - t.SetPressed = _IBSetP - t.SetDisabled= _IBSetD - t.Enabled = _IBSetE - t.ChangeIcon = null - t.UserAction = action - t.ChgState = _IBUI - t.mObjId = oId - t.mBorderId= bId - t.mWidth = w - t.mIsOn = t.mCurState = 0 -} -function _IBSetA() -{ - if( this.mIsOn ) { - obj=this.ChgState( gHiliteClr,gShadowClr,2 ) - obj.style.posTop=0 - } -} -function _IBSetI() -{ - if( this.mIsOn ) { - obj=this.ChgState( gFaceClr,gFaceClr,1 ) - obj.style.posTop=0 - } -} -function _IBSetP() -{ - if( this.mIsOn ) { - obj=this.ChgState( gShadowClr,gHiliteClr,2 ) - obj.style.posLeft+=1; obj.style.posTop+=1 - } -} -function _IBSetD() -{ - obj=this.ChgState( gFaceClr,gFaceClr,0 ) - obj.style.posTop=0 -} -function _IBSetE( state ) -{ - var t=this - GetObj( t.mBorderId ).style.visibility="visible" - if( state != t.mIsOn ) { - t.mIsOn=state - if( state ) - t.SetInactive() - else - t.SetDisabled() - } -} -function _IBP() -{ - var t=this - if( t.mIsOn ) { - if( t.UserAction != null ) - t.UserAction() - if( t.ChangeIcon ) { - obj=GetObj(t.mObjId) - if( t.ChangeIcon() ) - obj.style.posLeft=obj.style.posLeft+(t.mCurState-4)*t.mWidth - else - obj.style.posLeft=obj.style.posLeft+(t.mCurState-0)*t.mWidth - } - t.SetActive() - } -} -function _IBUI( clr1,clr2,nextState ) -{ - var t=this - SetBorder( GetObj( t.mBorderId ),clr1,clr2 ) - obj=GetObj( t.mObjId ) - obj.style.posLeft=obj.style.posLeft+(t.mCurState-nextState)*t.mWidth-obj.style.posTop - t.mCurState=nextState - return obj -} -function TxtBtn( oId,oeId,action,chkState ) -{ - var t=this - t.Perform = _TBP - t.SetActive = _TBSetA - t.SetInactive= _TBSetI - t.SetPressed = _TBSetP - t.SetDisabled= _TBSetD - t.SetEnabled = _TBSetE - t.GetState = chkState - t.UserAction = action - t.ChgState = _TBUI - t.mObjId = oId - t.m_elementsId= oeId - t.mIsOn = 1 -} -function _TBSetA() -{ - var t=this - if( t.mIsOn && !t.GetState() ) - t.ChgState( gHiliteClr,gShadowClr,0,0 ) -} -function _TBSetI() -{ - var t=this - if( t.mIsOn && !t.GetState() ) - t.ChgState( gFaceClr,gFaceClr,0,0 ) -} -function _TBSetP() -{ - if( this.mIsOn ) - this.ChgState( gShadowClr,gHiliteClr,1,1 ) -} -function _TBSetD() -{ - this.ChgState( gFaceClr,gFaceClr,0,0 ) - this.mIsOn = 0 -} -function _TBSetE() -{ - var t=this - if( !t.GetState() ) - t.ChgState( gFaceClr,gFaceClr,0,0 ) - else - t.ChgState( gShadowClr,gHiliteClr,1,1 ) - t.mIsOn = 1 -} -function _TBP() -{ - var t=this - if( t.mIsOn ) { - if( t.UserAction != null ) - t.UserAction() - if( t.GetState() ) - t.SetPressed() - else - t.SetActive() - } -} -function _TBUI( clr1,clr2,lOffset,tOffset ) -{ - SetBorder( GetObj( this.mObjId ),clr1,clr2 ) - Offset( GetObj( this.m_elementsId ),lOffset,tOffset ) -} -function GetObj( objId ){ return document.all.item( objId ) } -function Offset( obj, top, left ){ obj.style.top=top; obj.style.left=left } -function SetBorder( obj, upperLeft, lowerRight ) -{ - s=obj.style; - s.borderStyle = "solid" - s.borderWidth = 1 - s.borderLeftColor = s.borderTopColor = upperLeft - s.borderBottomColor= s.borderRightColor = lowerRight -} -function GetBtnObj(){ return gBtnArr[window.event.srcElement.id] } -function BtnOnOver(){ b=GetBtnObj(); if( b != null ) b.SetActive() } -function BtnOnDown(){ b=GetBtnObj(); if( b != null ) b.SetPressed() } -function BtnOnOut(){ b=GetBtnObj(); if( b != null ) b.SetInactive() } -function BtnOnUp() -{ - b=GetBtnObj() - if( b != null ) - b.Perform() - else - Upd() -} -function GetNtsState(){ return parent.gNtsOpen } -function GetOtlState(){ return parent.gOtlOpen } -function GetOtlTxtState(){ return parent.gOtlTxtExp } -function NtsBtnSetFlag( fVal ) -{ - s=document.all.item( this.m_flagId ).style - s.display="none" - if( fVal ) - s.display="" - else - s.display="none" -} - -var gHiliteClr="THREEDHIGHLIGHT",gShadowClr="THREEDSHADOW",gFaceClr="THREEDFACE" -var gBtnArr = new Array() -gBtnArr["nb_otl"] = new TxtBtn( "nb_otl","nb_otlElem",parent.ToggleOtlPane,GetOtlState ) -gBtnArr["nb_nts"] = new TxtBtn( "nb_nts","nb_ntsElem",parent.ToggleNtsPane,GetNtsState ) -gBtnArr["nb_prev"]= new ImgBtn( "nb_prev","nb_prevBorder",30,parent.GoToPrevSld ) -gBtnArr["nb_next"]= new ImgBtn( "nb_next","nb_nextBorder",30,parent.GoToNextSld ) -gBtnArr["nb_sldshw"]= new ImgBtn( "nb_sldshw","nb_sldshwBorder",18,parent.FullScreen ) -gBtnArr["nb_voice"] = new ImgBtn( "nb_voice","nb_voiceBorder",18,parent.ToggleVNarration ) -gBtnArr["nb_otlTxt"]= new ImgBtn( "nb_otlTxt","nb_otlTxtBorder",23,parent.ToggleOtlText ) -gBtnArr["nb_nts"].m_flagId= "notes_flag" -gBtnArr["nb_nts"].SetFlag = NtsBtnSetFlag -gBtnArr["nb_otlTxt"].ChangeIcon= GetOtlTxtState -var sNext="Next",sPrev="Previous",sEnd="End Show",sFont="Arial", alwaysOn = false -function ShowMenu() -{ - BuildMenu(); - var doc=PPTSld.document.body,x=PPTSld.event.clientX+doc.scrollLeft,y=PPTSld.event.clientY+doc.scrollTop - - m = PPTSld.document.all.item("ctxtmenu") - m.style.pixelLeft=x - if( (x+m.scrollWidth > doc.clientWidth)&&(x-m.scrollWidth > 0) ) - m.style.pixelLeft=x-m.scrollWidth - - m.style.pixelTop=y - if( (y+m.scrollHeight > doc.clientHeight)&&(y-m.scrollHeight > 0) ) - m.style.pixelTop=y-m.scrollHeight - - m.style.display="" -} -function _CM() -{ - if( !parent.IsFullScrMode() && !alwaysOn) return; - - if(!PPTSld.event.ctrlKey) { - ShowMenu() - return false - } else - HideMenu() -} - -function processNavKPH(event) { - if ( PPTSld && (event.keyCode != 13 || !event.srcElement.href || event.srcElement.href == "" ) ) - return PPTSld._KPH(event); -} -function processNavClick() { - HideMenu(); - return true; -} -function BuildMenu() -{ - if( PPTSld.document.all.item("ctxtmenu") ) return - - var mObj=CreateItem( PPTSld.document.body ) -mObj.id="ctxtmenu" - var s=mObj.style - s.position="absolute" - s.cursor="default" - s.width="100px" - SetCMBorder(mObj,"menu","black") - - var iObj=CreateItem( mObj ) - SetCMBorder( iObj, "threedhighlight","threedshadow" ) - iObj.style.padding=2 - if ( self.IsFullScrMode() ) { - CreateMenuItem( iObj,sNext,M_GoNextSld,M_True ) - CreateMenuItem( iObj,sPrev,M_GoPrevSld,M_HasPrevSld ) - } - else { - CreateMenuItem( iObj,sNext, base.TP_GoToNextSld, base.HasNextSld ) - CreateMenuItem( iObj,sPrev,base.GoToPrevSld, base.HasPrevSld ) - } - var sObj=CreateItem( iObj ) - SetCMBorder(sObj,"menu","menu") - var s=sObj.style - s.borderTopColor="threedshadow" - s.borderBottomColor="threedhighlight" - s.height=1 - s.fontSize="0px" - if ( self.IsFullScrMode() ) - CreateMenuItem( iObj,sEnd,M_End,M_True ) - else - CreateMenuItem( iObj,sEnd,M_End,M_False ) -} -function Highlight() { ChangeClr("activecaption","threedhighlight") } -function Deselect() { ChangeClr("threedface","menutext") } -function Perform() -{ - e=PPTSld.event.srcElement - if( e.type=="menuitem" && e.IsActive() ) - e.Action() - else - PPTSld.event.cancelBubble=true -} -function ChangeClr( bg,clr ) -{ - e=PPTSld.event.srcElement - if( e.type=="menuitem" && e.IsActive() ) { - e.style.backgroundColor=bg - e.style.color=clr - } -} - -function M_HasPrevSld() { return( base.HasPrevSld() ) } -function M_GoNextSld() { - base.SetFSMode(1); - if( gIsEndShow ) - M_End(); - else { - if ( base.HasNextSld() ) - base.GoToNextSld(); - else if ( base.EndSlideShow ) { - StartEndShow(); - gIsEndShow = 1; - - PPTNav.location.reload(); - } - else - base.CloseFullScreen(); - } -} -function M_GoPrevSld() { - base.SetFSMode(1); - g_hideNav = 0; - if( gIsEndShow ) { - gIsEndShow = 0; - if ( base.msie > 0 && IsMac() ) - ChangeFrame( SLIDE_FRAME, GetHrefObj( g_currentSlide ).m_slideHref ); - else - PPTSld.history.back(); - - PPTNav.location.reload(); - if( PPTSld.event ) - PPTSld.event.cancelBubble=true; - } - else - base.GoToPrevSld(); -} -function M_True() { return true } -function M_False() { return false } - -function M_End() { - base.CloseFullScreen(); - /*PPTSld.event.cancelBubble=true; - window.close( self )*/ -} - -function CreateMenuItem( node,text,action,eval ) -{ - var e=CreateItem( node ) - e.type="menuitem" - e.Action=action - e.IsActive=eval - e.innerHTML=text - - if( !e.IsActive() ) - e.style.color="threedshadow" - e.onclick=Perform - e.onmouseover=Highlight - e.onmouseout=Deselect - s=e.style; - s.fontFamily=sFont - s.fontSize="8pt" - s.paddingLeft=2 -} -function CreateItem( node ) -{ - var elem=PPTSld.document.createElement("DIV") - node.insertBefore( elem ) - return elem -} -function SetCMBorder( o,ltClr,rbClr ) -{ - var s=o.style - s.backgroundColor="menu" - s.borderStyle="solid" - s.borderWidth=1 - s.borderColor=ltClr+" "+rbClr+" "+rbClr+" "+ltClr -} - -/* netscape context menu */ -g_ctxmenu = 0; -function setRect( obj, X, Y, W, H ) { - obj.top = Y; - obj.left = X; - obj.clip.top = 0; - obj.clip.left = 0; - obj.clip.bottom = H; - obj.clip.right = W; -} - -function KPH(event) { - if ( ! base.IsFullScrMode() && !alwaysOn ) - return true; - - if ( (!IsMac() &&event.which == 3) || ( IsMac() && (event.modifiers & Event.CONTROL_MASK) && event.which == 1 ) ) { - PPTSld.g_ctxmenu = 1; - PPTSld.stripUobj.visibility = "show"; - PPTSld.stripDobj.visibility = "show"; - PPTSld.shadeUobj.visibility = "show"; - PPTSld.shadeDobj.visibility = "show"; - PPTSld.panelobj.visibility = "show"; - PPTSld.Fobj.visibility = "show"; - PPTSld.Bobj.visibility = "show"; - PPTSld.Eobj.visibility = "show"; - - setRect(PPTSld.shadeUobj, event.pageX-2, event.pageY-2, 82, 67 ); - setRect(PPTSld.shadeDobj, event.pageX, event.pageY, 82, 67 ); - setRect(PPTSld.panelobj, event.pageX, event.pageY, 80, 65 ); - setRect(PPTSld.Fobj, event.pageX, event.pageY, 80, 20 ); - setRect(PPTSld.Bobj, event.pageX, event.pageY+20, 80, 20 ); - setRect(PPTSld.stripUobj, event.pageX, event.pageY+41, 80, 1 ); - setRect(PPTSld.stripDobj, event.pageX, event.pageY+43, 80, 1 ); - setRect(PPTSld.Eobj, event.pageX, event.pageY+45, 80, 20 ); - return false; - } - if ( HitOK( event ) ) { - PPTSld.g_ctxmenu = 0; - PPTSld.stripUobj.visibility = "hide"; - PPTSld.stripDobj.visibility = "hide"; - PPTSld.shadeUobj.visibility = "hide"; - PPTSld.shadeDobj.visibility = "hide"; - PPTSld.panelobj.visibility = "hide"; - PPTSld.Fobj.visibility = "hide"; - PPTSld.Bobj.visibility = "hide"; - PPTSld.Eobj.visibility = "hide"; - } - return true; -} - -function overMe() { - this.bgColor = "blue"; -} - -function outMe() { - this.bgColor = "#AAAAAA"; -} - -function makeElement( whichEl, whichContainer ) { - if ( arguments.length == 1 ) { - whichContainer = PPTSld; - } - tmp = new Layer(100,whichContainer); - eval( whichEl + " = tmp" ); - return eval(whichEl); -} - -function initMe( obj, clr, text ) { - obj.bgColor = clr; -// obj.document.write("<a href='javascript:return false'>" + text + "</a>"); - obj.document.write( "<font size=2 face=Arial " ); - if ( !M_HasPrevSld() && (obj == PPTSld.Bobj ) ) { - obj.document.write( " color='#808080' " ); - } - else { - obj.onmouseover = overMe; - obj.onmouseout = outMe; - } - obj.document.write( " >   " + text +"</font> <layer top=0 left=0 width=100 height=40 ></layer>"); - obj.document.close(); - obj.captureEvents(Event.CLICK); - obj.color = "black"; -} - -function createCM() { - if ( base.IsFullScrMode() ) { - var clr = "#AAAAAA"; - PPTSld.shadeUobj = makeElement("SHADEU"); - PPTSld.shadeDobj = makeElement("SHADED"); - PPTSld.panelobj = makeElement("PANEL"); - PPTSld.stripUobj = makeElement("STRIPU"); - PPTSld.stripDobj = makeElement("STRIPD"); - PPTSld.shadeUobj.bgColor = "#BBBBBB"; - PPTSld.shadeDobj.bgColor = "#888888"; - PPTSld.stripUobj.bgColor = "#777777"; - PPTSld.stripDobj.bgColor = "#CCCCCC"; - PPTSld.panelobj.bgColor = clr; - PPTSld.Fobj = makeElement("Next"); - PPTSld.Bobj = makeElement("Previous"); - PPTSld.Eobj = makeElement("EndShow"); - initMe( PPTSld.Fobj, clr, "Next" ); - PPTSld.Fobj.onclick = M_GoNextSld; - - initMe( PPTSld.Bobj, clr, "Previous" ); - PPTSld.Bobj.onclick = M_GoPrevSld; - - initMe( PPTSld.Eobj, clr, "End Show"); - PPTSld.Eobj.onclick = base.CloseFullScreen; - } -} - -function IsContextMenu() { - return (g_ctxmenu == 1) -} -var g_notesTable = new Array() -var g_hiddenSlide = new Array() -makeSlide( 0,1,1); -makeSlide( 1,1,1); -makeSlide( 2,1,1); -makeSlide( 3,1,1); -makeSlide( 4,1,1); -makeSlide( 5,1,1); -makeSlide( 6,1,1); -makeSlide( 7,1,1); -makeSlide( 8,1,1); -makeSlide( 9,1,1); -makeSlide( 10,1,1); -makeSlide( 11,0,1); -makeSlide( 12,0,1); -makeSlide( 13,1,1); - -var END_SHOW_HREF = "endshow.htm", - OUTLINE_EXPAND_HREF = "outline_expanded.htm", - OUTLINE_COLLAPSE_HREF = "outline_collapsed.htm", - OUTLINE_NAVBAR_HREF = "outline_navigation_bar.htm", - NAVBAR_HREF = "navigation_bar.htm", - BLANK_NOTES_HREF = "blank_notes.htm", - NUM_VISIBLE_SLIDES = 14, - SIMPLE_FRAMESET = 0, - SLIDE_FRAME = "PPTSld", - NOTES_FRAME = "PPTNts", - OUTLINE_FRAME = "PPTOtl", - OUTLINE_NAVBAR_FRAME = "PPTOtlNav", - NAVBAR_FRAME = "PPTNav", - MAIN_FRAME = "MainFrame", - FS_NAVBAR_HREF = "fs_navigation_bar.htm", - isIEFiles = 2, - isNAVFiles = 8, - isFLATFiles = 16, - includeNotes = 1, - PPTPRESENTATION = 1; -var INITSLIDENUM = 1; - -var EndSlideShow = 0; -var g_outline_href = OUTLINE_COLLAPSE_HREF; -var g_fullscrMode = 0; -var FSWin = null; -var gtmpstr = document.location.href; -var g_baseURL = gtmpstr.substr(0, gtmpstr.lastIndexOf("/") ) + "/" + "webqtl_demo2.ppt_files"; -var g_showoutline = 1; -var g_shownotes = includeNotes; -var g_currentSlide = INITSLIDENUM, g_prevSlide = INITSLIDENUM; -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 ); 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- 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); 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- } - 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( 14 ); - 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( 14 ); - } - else - window.location.replace( "webqtl_demo2.ppt_files/error.htm" ); - } - else { - if ( isNAVFiles > 0 && ver < 5) - navArray( 14 ); - 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( 14 ); - } - else - window.location.replace( "webqtl_demo2.ppt_files/error.htm" ); - } -} -else { - /* - if ( IsFramesMode() && !isWebTV() ) - StatusPlay("This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator."); - */ - if ( isFLATFiles <= 0 ) { - /* if ( IsFramesMode() ) - window.alert("This presentation contains content that your browser may not be able to display properly. This presentation is optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); - */ - window.location.replace( "webqtl_demo2.ppt_files/error.htm" ); - } - /* - else if ( IsFramesMode() && !isWebTV() ) - StatusPlay( "This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); - */ - jpegArray ( 14 ); - } - -} - -function isWebTV() { - if ( window.navigator.appName.indexOf( 'WebTV' ) >= 0 ) - return true; - return false; -} - -var count; -var statusText; -var statusfirst = 0; - function display50( text ) -{ - len = text.length; - if ( len < 50 && count < 2) { - window.status = text; - window.setTimeout( "repeat()", 300 ); - } - else { - var period = 200; - window.status = text; - newtext = text.substring( 1, len ); - if ( statusfirst ) { - statusfirst = 0; - period = 2000; - } - window.setTimeout( "display50( newtext )", period ); - } -} -function repeat( ) { - count++; - statusfirst = 1; - display50( statusText ); -} - -function StatusPlay( text ) { - count = 0; - statusText = text; - repeat( ); - } -function makeSlide( i, notes, visible ) { - g_notesTable[i] = notes; - g_hiddenSlide[i] = visible; -} - diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm deleted file mode 100755 index 11938baa..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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"> </span><br> </span></span><span style='position:absolute;top:48.68%;left:4.34%;width:95.23%'><span style='font-size:73%'>link to www.genenetwork.org</span><span style='font-size: 73%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <div style='position:absolute;top:24.02%;left:5.82%;width:54.03%;height:68.55%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='position:absolute;top:0%;left:3.67%;width:96.32%; height:61.34%'> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:0%;width:100.0%;height:51.68%'><span style='position:absolute;top:0%;left:0%;width:89.05%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 1. How to study </span></span><span style='position:absolute;top:23.57%; left:9.66%;width:79.13%'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>expression variation </span></span><span style='position:absolute; top:47.15%;left:9.66%;width:90.33%'><span style='font-size:94%;color:#E9EB5D; mso-color-index:3'>and genetic correlation </span></span><span style='position:absolute;top:70.73%;left:9.66%;width:79.13%'><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>(slides 2–17)<br> </span></span></div> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:60.5%;left:0%;width:93.63%;height:39.91%'><span style='position:absolute;top:0%;left:0%;width:95.1%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering </span></span><span style='position:absolute;top:30.52%; left:10.32%;width:89.67%'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>upstream modulators </span></span><span style='position:absolute;top:61.05%; left:10.32%;width:84.51%'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 18–29)</span></span></div> </div> </div> <img border=0 src="slide0001_image001.png" style='position:absolute;top:17.84%; left:74.17%;width:23.57%;height:64.31%'> <div class=O style='position:absolute;top:75.44%;left:74.56%;width:10.46%; height:14.48%'> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:42.68%'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:45.12%;left:0%;width:82.27%;height:54.87%'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:82.15%;left:4.1%;width:96.15%;height:18.19%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'></div> <img border=0 src="slide0001_image002.png" style='position:absolute;top:50.53%; left:48.74%;width:25.56%;height:13.07%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Part 2: Discovering upstream modulators and quantitative trait loci (QTLs). A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </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 deleted file mode 100755 index a1cb20e4..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image001.png +++ /dev/null Binary files differdiff --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 deleted file mode 100755 index e06bd0db..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_image002.png +++ /dev/null Binary files differdiff --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 deleted file mode 100755 index 9e0445f3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0001_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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 deleted file mode 100755 index b40dd6e1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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 ) ) { - 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="master05_background.png" v:shapes="_x0000_s3075" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div class=O style='position:absolute;top:92.93%;left:8.74%;width:18.67%; height:5.83%'> <div style='mso-line-spacing:"-134 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.48%'><span style='font-family:Times;font-size:117%;color:white;display:none'><br> </span></div> <div style='mso-line-spacing:"-134 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.51%;left:0%;width:100.0%;height:48.48%'><span style='font-family:Times;font-size:117%;color:white;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:92.93%;left:35.49%;width:29.4%; height:5.83%'> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.48%'><span style='font-family:Times;font-size:117%;color:white; display:none'><br> </span></div> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:51.51%;left:0%;width:100.0%; height:48.48%'><span style='font-family:Times;font-size:117%;color:white; mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:2.12%;left:-5.43%;width:105.96%;height:11.13%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:0%;left:0%;width:100.0%;height:92.06%'> <div style='text-align:center;mso-line-spacing:"-240 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16;position:absolute;top:0%;left:0%;width:100.0%; height:65.51%'><span style='font-family:Arial;font-size:267%;color:#E9EB5D'>How to make recombinant inbred strains (RI)</span><span style='font-family:Arial; font-size:150%;color:aqua;display:none'><br> </span></div> <div style='text-align:center;mso-line-spacing:"-160 0 0";mso-margin-left-alt: 16;mso-text-indent-alt:16;position:absolute;top:62.06%;left:6.37%;width:87.37%; height:37.93%'><span style='font-family:Arial;font-size:150%;color:aqua; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image003.png" style='position:absolute;top:28.79%; left:45.43%;width:18.14%;height:1.06%'><img border=0 src="slide0002_image004.png" style='position:absolute;top:20.31%;left:28.21%; width:1.98%;height:11.83%'> <div style='position:absolute;top:15.01%;left:25.03%;width:19.47%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:6.8%;width:93.19%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>C57BL/6J (B)<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:83.21%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image005.png" style='position:absolute;top:20.31%; left:30.46%;width:1.98%;height:11.83%'> <div style='position:absolute;top:15.01%;left:62.25%;width:16.55%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:8.0%;width:92.8%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J (D)<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:82.75%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image006.png" style='position:absolute;top:20.31%; left:66.62%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image007.png" style='position:absolute;top:35.51%;left:23.97%; width:50.86%;height:1.23%'><img border=0 src="slide0002_image008.png" style='position:absolute;top:35.68%;left:24.1%;width:.66%;height:4.06%'><img border=0 src="slide0002_image009.png" style='position:absolute;top:35.68%; left:40.92%;width:.52%;height:4.06%'><img border=0 src="slide0002_image010.png" style='position:absolute;top:35.68%;left:57.61%;width:.52%;height:4.06%'><img border=0 src="slide0002_image011.png" style='position:absolute;top:35.68%; left:74.3%;width:.52%;height:3.88%'> <div style='position:absolute;top:42.75%;left:5.69%;width:6.49%;height:12.36%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:8.57%;left:20.4%;width:73.46%; height:84.28%'> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F1<br> </b></span></div> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.84%;left:0%;width:83.33%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:lastCR; display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0002_image012.png" style='position:absolute;top:39.92%; left:22.25%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image013.png" style='position:absolute;top:39.92%;left:38.94%; width:4.23%;height:11.83%'><img border=0 src="slide0002_image014.png" style='position:absolute;top:39.92%;left:55.62%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image015.png" style='position:absolute;top:39.39%; left:72.84%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image016.png" style='position:absolute;top:43.46%;left:43.97%; width:11.12%;height:3.53%'><img border=0 src="slide0002_image017.png" style='position:absolute;top:60.95%;left:20.66%;width:9.8%;height:3.53%'> <div style='position:absolute;top:71.73%;left:58.41%;width:20.26%;height:26.67%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:12.58%;left:6.53%;width:88.23%; height:83.44%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:69.84%'><span style='position:absolute;top:0%;left:0%;width:99.25%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'><b>20 generations </b></span></span><span style='position:absolute;top:39.77%;left:0%;width:100.0%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'><b>brother-sister </b></span></span><span style='position:absolute;top:80.68%;left:0%;width:99.25%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'><b>matings</b></span><span style='font-family:Arial;font-size:233%;color:#FFFF99;display:none'><b><br> </b></span></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:73.8%;left:0%;width:99.25%; height:26.98%'><span style='font-family:Arial;font-size:233%;color:#FFFF99; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0002_image018.png" style='position:absolute;top:60.95%; left:50.72%;width:9.93%;height:3.53%'><img border=0 src="slide0002_image019.png" style='position:absolute;top:62.72%;left:54.03%;width:4.37%;height:28.97%'><img border=0 src="slide0002_image020.png" style='position:absolute;top:61.13%; left:79.86%;width:10.86%;height:3.53%'><img border=0 src="slide0002_image021.png" style='position:absolute;top:62.36%;left:83.97%; width:4.1%;height:28.79%'> <div style='position:absolute;top:92.93%;left:21.72%;width:9.27%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:12.85%;width:85.71%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD1</span><span style='font-family:Arial;font-size:150%;color:#484848;display:none'><br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:83.33%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#484848;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:92.75%;left:51.78%;width:9.27%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:12.85%;width:85.71%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD2<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:83.33%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:92.93%;left:80.79%;width:10.99%;height:5.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:15.62%;left:12.04%;width:87.95%; height:68.75%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD80</span></div> </div> <div style='position:absolute;top:90.45%;left:64.1%;width:17.74%;height:17.49%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:6.06%;left:7.46%;width:92.53%; height:88.88%'> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.86%'><span style='font-family:Arial;font-size:300%;color:#FFFF99'>+ É +<br> </span></div> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.0%;left:0%;width:83.87%;height:48.86%'><span style='font-family:Arial;font-size:300%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:62.89%;left:4.9%;width:6.49%;height:12.36%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.14%;left:20.4%;width:73.46%; height:84.28%'> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F2<br> </b></span></div> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.84%;left:0%;width:83.33%;height:49.15%'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format:lastCR; display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0002_image022.png" style='position:absolute;top:54.24%; left:18.01%;width:75.62%;height:1.06%'><img border=0 src="slide0002_image023.png" style='position:absolute;top:54.06%;left:17.88%; width:.66%;height:3.88%'><img border=0 src="slide0002_image024.png" style='position:absolute;top:54.24%;left:32.45%;width:.52%;height:3.88%'><img border=0 src="slide0002_image025.png" style='position:absolute;top:54.24%; left:48.07%;width:.52%;height:4.06%'><img border=0 src="slide0002_image026.png" style='position:absolute;top:54.24%;left:62.78%;width:.52%;height:4.06%'><img border=0 src="slide0002_image027.png" style='position:absolute;top:54.24%; left:77.74%;width:.52%;height:4.06%'><img border=0 src="slide0002_image028.png" style='position:absolute;top:54.59%;left:92.71%;width:.52%;height:3.71%'><img border=0 src="slide0002_image029.png" style='position:absolute;top:44.87%; left:49.13%;width:.79%;height:10.07%'><img border=0 src="slide0002_image030.png" style='position:absolute;top:57.59%;left:15.89%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image031.png" style='position:absolute;top:57.59%; left:30.86%;width:4.37%;height:11.83%'><img border=0 src="slide0002_image032.png" style='position:absolute;top:57.59%;left:46.35%; width:4.23%;height:11.83%'><img border=0 src="slide0002_image033.png" style='position:absolute;top:57.59%;left:60.92%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image034.png" style='position:absolute;top:57.59%; left:75.62%;width:4.23%;height:11.83%'><img border=0 src="slide0002_image035.png" style='position:absolute;top:57.59%;left:90.86%; width:4.23%;height:11.83%'><img border=0 src="slide0002_image036.png" style='position:absolute;top:84.09%;left:56.42%;width:1.98%;height:1.41%'><img border=0 src="slide0002_image037.png" style='position:absolute;top:80.21%; left:25.96%;width:1.98%;height:11.83%'><img border=0 src="slide0002_image038.png" style='position:absolute;top:84.98%;left:86.09%; width:1.85%;height:2.12%'> <div style='position:absolute;top:75.61%;left:1.58%;width:13.9%;height:13.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.69%;left:.95%;width:99.04%; height:85.89%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.69%;width:83.65%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'><b>BXD RI<br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'><b>Strain set<br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.69%;width:83.65%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> </div> <img border=0 src="slide0002_image039.png" style='position:absolute;top:12.36%; left:14.17%;width:10.59%;height:6.36%'><img border=0 src="slide0002_image040.png" style='position:absolute;top:10.6%;left:76.42%; width:14.3%;height:8.3%'> <div style='position:absolute;top:20.84%;left:17.48%;width:9.53%;height:13.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.69%;left:6.94%;width:88.88%; height:85.89%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.81%;width:82.81%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>fully<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>inbred<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.81%;width:82.81%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:38.16%;left:2.91%;width:11.78%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:3.37%;width:94.38%; height:81.81%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>isogenic<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:51.11%;left:8.33%;width:83.33%; height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:54.41%;left:1.85%;width:12.18%;height:13.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:7.69%;left:2.17%;width:95.65%; height:85.89%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:7.95%;width:84.09%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>hetero-<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.83%;left:0%;width:100.0%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>geneous<br> </span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:67.16%;left:7.95%;width:84.09%; height:32.83%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:74.91%;left:29.0%;width:21.98%;height:21.73%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:4.06%;left:5.42%;width:89.15%; height:91.86%'> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:79.64%'><span style='position:absolute;top:0%;left:.67%;width:99.32%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>Recombined </span></span><span style='position:absolute;top:25.55%;left:.67%;width:99.32%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>chromosomes </span></span><span style='position:absolute;top:51.11%;left:0%;width:100.0%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>are needed for </span></span><span style='position:absolute;top:75.55%;left:.67%;width:99.32%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>mapping<br> </span></span></div> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:80.53%;left:.67%;width:99.32%; height:19.46%'><span style='font-family:Arial;font-size:150%;color:#FFFF99; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:10.24%;left:25.56%;width:10.46%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:12.65%;width:87.34%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>female<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:84.05%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:10.24%;left:64.5%;width:7.94%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:9.09%;left:15.0%;width:83.33%; height:81.81%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>male<br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:51.11%;left:0%;width:84.0%;height:48.88%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:30.56%;left:78.01%;width:19.47%;height:9.71%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:16.36%;left:6.12%;width:93.19%; height:74.54%'> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:41.46%'><span style='font-family:Arial;font-size:117%;color:#FFFF99'>chromosome pair</span><span style='font-family:Arial;font-size:150%;color:#FFFF99;display:none'><br> </span></div> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:46.34%;left:0%;width:83.21%;height:53.65%'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format:lastCR; display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image041.png" style='position:absolute;top:31.09%; left:65.82%;width:12.84%;height:2.82%'> <div style='position:absolute;top:86.21%;left:3.97%;width:9.8%;height:14.13%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:5.0%;left:5.4%;width:90.54%; height:87.5%'> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:8.95%;width:82.08%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>Inbred<br> </span></div> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:25.71%;left:0%;width:100.0%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>Isogenic<br> </span></div> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:50.0%;left:4.47%;width:89.55%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:#E9EB5D'>siblings</span><span style='font-family:Arial;font-size:117%;color:aqua;display:none'><br> </span></div> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:75.71%;left:8.95%;width:82.08%; height:24.28%'><span style='font-family:Arial;font-size:117%;color:aqua; mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0002_image042.png" style='position:absolute;top:79.32%; left:83.84%;width:1.98%;height:11.83%'><img border=0 src="slide0002_image043.png" style='position:absolute;top:84.8%;left:83.7%; width:1.85%;height:2.12%'><img border=0 src="slide0002_image044.png" style='position:absolute;top:79.85%;left:53.5%;width:1.98%;height:11.83%'><img border=0 src="slide0002_image045.png" style='position:absolute;top:83.92%; left:53.5%;width:1.98%;height:1.41%'><img border=0 src="slide0002_image046.png" style='position:absolute;top:80.21%;left:23.44%;width:1.98%;height:11.83%'> <div style='position:absolute;top:18.72%;left:43.04%;width:13.77%;height:9.54%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:11.11%;left:9.61%;width:90.38%; height:79.62%'><span style='font-family:Arial;font-size:300%;color:aqua'>B</span><span style='font-family:Arial;font-size:300%;color:#FFFF99'>X</span><span style='font-family:Arial;font-size:300%;color:#FF1911'>D</span></div> </div> <img border=0 src="slide0002_image047.png" style='position:absolute;top:27.2%; left:32.98%;width:31.39%;height:4.06%'><img border=0 src="slide0002_image048.png" style='position:absolute;top:66.25%;left:60.92%; width:1.98%;height:3.18%'><img border=0 src="slide0002_image049.png" style='position:absolute;top:64.31%;left:15.89%;width:1.98%;height:5.3%'><img border=0 src="slide0002_image050.png" style='position:absolute;top:57.59%; left:75.62%;width:1.98%;height:5.65%'><img border=0 src="slide0002_image051.png" style='position:absolute;top:28.44%;left:48.87%;width:.92%;height:8.12%'><img border=0 src="slide0002_image052.png" style='position:absolute;top:62.19%; left:23.84%;width:3.57%;height:16.96%'><img border=0 src="slide0002_image053.png" style='position:absolute;top:61.48%;left:63.17%; width:1.98%;height:8.12%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. Over the last decade, our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD strains. They have all been genotyped using about 13,700 markers (SNPs and microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ regions of the chromosomes as shown in the figure above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Chromosomes of RI GRPs usually have about 4 times as many recombinations as those of F2 animals. However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50 RI strains contain as many recombinations as 100 F2 animals.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. BXD43 through BXD100 were generated using a special method that resulted in a further doubling of the average recombination density per chromosome. The entire set of 80 BXDs therefore contains as many recombinations as about 260 F2 animals.</font><br> </td> </tr> </table> </div> <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/slide0002_image002.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002_image002.png deleted file mode 100755 index 2eb797be..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002_image002.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002_image003.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002_image003.png deleted file mode 100755 index 6cb8411f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002_image003.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0002_image004.png 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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>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <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 diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003.htm deleted file mode 100755 index 2c4a0620..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0003.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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="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.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0003_image054.png" style='position:absolute;top:40.45%; left:73.24%;width:14.56%;height:5.3%'> <div class=O style='position:absolute;top:40.81%;left:74.56%;width:11.92%; height:7.24%'> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white'>aa<br> </span></div> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:41.46%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format:lastCR; display:none'><br> </span></div> </div> <img border=0 src="slide0003_image055.png" style='position:absolute;top:16.6%; left:73.24%;width:14.56%;height:5.3%'> <div class=O style='position:absolute;top:16.96%;left:74.56%;width:11.92%; height:7.24%'> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white'>aaaa<br> </span></div> <div style='mso-line-spacing:"-126 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:41.46%;left:0%;width:100.0%;height:60.97%'><span style='font-family:Gadget;font-size:150%;color:white;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div style='position:absolute;top:20.31%;left:71.65%;width:25.96%;height:19.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.0%;left:5.1%;width:95.4%; height:84.54%'> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:#E2EBF0'>D2 strain</span><span style='font-family: Palatino;font-size:333%;color:#FBFDB8;display:none'><br> </span></div> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:49.46%;left:0%;width:88.77%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#FBFDB8;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:43.81%;left:71.65%;width:25.56%;height:19.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.9%;left:5.18%;width:94.81%; height:84.54%'> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:#F6BF69'>B6 strain</span><span style='font-family: Palatino;font-size:333%;color:#F6BF69;display:none'><br> </span></div> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:48.38%;left:0%;width:87.43%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#F6BF69;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0003_image056.png" style='position:absolute;top:17.31%; left:31.25%;width:1.32%;height:42.22%'><img border=0 src="slide0003_image057.png" style='position:absolute;top:40.63%;left:31.39%; width:39.86%;height:3.53%'> <div style='position:absolute;top:20.67%;left:38.27%;width:30.19%;height:26.32%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:6.04%;left:4.38%;width:92.1%; height:89.93%'> <div style='mso-line-spacing:"-320 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:58.2%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size: 233%;color:#E9EB5D'><i>amount of </i></span></span><span style='position:absolute; top:53.84%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'><i>transcript</i></span><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;display:none'><br> </span></span></div> <div style='mso-line-spacing:"-422 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:61.19%;left:0%;width:100.0%;height:38.8%'><span style='font-family:Palatino;font-size:367%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:6.0%;left:72.45%;width:21.05%;height:19.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.0%;left:6.28%;width:88.67%; height:84.54%'> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:white'>4 </span><span style='font-size:233%; color:white'>units</span><span style='font-family:Palatino;font-size:333%; color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:49.46%;left:0%;width:100.0%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:29.5%;left:72.45%;width:21.05%;height:19.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:10.9%;left:6.28%;width:88.67%; height:84.54%'> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:45.16%'><span style='font-size:267%;color:white'>2</span><span style='font-size:233%; color:white'> units</span><span style='font-family:Palatino;font-size:333%; color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:"-384 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:48.38%;left:0%;width:100.0%;height:50.53%'><span style='font-family:Palatino;font-size:333%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0003_image058.png" style='position:absolute;top:15.72%; left:31.25%;width:40.26%;height:5.47%'> <div class=O style='position:absolute;top:17.84%;left:9.93%;width:4.76%; height:16.43%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:83.33%;height:50.53%'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:17.84%;left:17.88%;width:4.23%; height:16.43%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:84.37%;height:50.53%'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:79.5%;left:5.43%;width:104.1%;height:13.6%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='mso-line-spacing:"-256 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:3.89%;left:1.27%;width:98.72%; height:93.5%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-size:233%;color:#E2EBF0'>D</span><span style='font-size:233%; color:#E9EB5D'> </span><span style='font-size:200%;color:#E9EB5D'>and </span><span style='font-size:233%;color:#F6BF69'>B</span><span style='font-size:233%; color:#E9EB5D'> </span><span style='font-size:200%;color:#E9EB5D'>may be SNP-like variants in the promoter </span></span><span style='position:absolute; top:34.72%;left:0%;width:99.74%'><span style='font-size:200%;color:#E9EB5D'>itself (cis QTL) or in </span><span style='font-size:200%;color:#EAEC5E'>upstream genes (trans QTLs)</span><span style='font-size:300%;color:#E9EB5D'>.</span></span></div> </div> <div class=O style='position:absolute;top:7.59%;left:4.23%;width:22.78%; height:16.25%'> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:1.74%;width:97.09%; height:33.69%'><span style='font-size:200%;color:#E9EB5D'>UPSTREAM<br> </span></div> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:32.6%;left:0%;width:100.0%; height:33.69%'><span style='font-size:200%;color:#E9EB5D'>modulators<br> </span></div> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:66.3%;left:4.65%;width:90.69%; height:33.69%'><span style='font-size:200%;color:#E9EB5D;mso-special-format: lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:7.59%;left:44.5%;width:16.95%;height:17.84%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:3.96%;left:7.03%;width:85.15%; height:92.07%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0'>High<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16;position:absolute;top:49.46%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:63.78%;left:8.74%;width:6.35%;height:17.84%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:3.96%;left:20.83%;width:75.0%; height:92.07%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:83.33%;height:50.53%'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:63.78%;left:15.09%;width:5.96%;height:17.84%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:3.96%;left:20.0%;width:71.11%; height:92.07%'> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.53%'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:49.46%;left:0%;width:84.37%;height:50.53%'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div style='position:absolute;top:71.02%;left:7.54%;width:16.02%;height:12.54%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:5.63%;left:7.43%;width:91.73%; height:87.32%'> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.0%'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:48.38%;left:0%;width:82.88%;height:50.0%'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <img border=0 src="slide0003_image059.png" style='position:absolute;top:57.24%; left:-1.05%;width:101.98%;height:7.59%'> <div class=O style='position:absolute;top:44.16%;left:47.15%;width:9.4%; height:12.72%'> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:51.38%'><span style='font-size:233%;color:#F6BF69'>Low<br> </span></div> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:50.0%;left:0%;width:83.09%;height:51.38%'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR;display:none'><br> </span></div> </div> <div style='position:absolute;top:58.12%;left:.79%;width:113.37%;height:6.36%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;position:absolute;top:11.11%;left:1.16%;width:98.83%; height:75.0%'><span style='font-family:Gadget;font-size:167%;color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR >>>>></span></div> </div> <img border=0 src="slide0003_image060.png" style='position:absolute;top:37.98%; left:8.6%;width:13.77%;height:20.67%'> <div class=O style='position:absolute;top:40.28%;left:10.99%;width:1.72%; height:11.48%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:50.76%;left:7.69%;width:84.61%; height:50.76%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <div class=O style='position:absolute;top:40.63%;left:18.41%;width:1.72%; height:11.48%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:49.23%;left:7.69%;width:84.61%; height:50.76%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <img border=0 src="slide0003_image061.png" style='position:absolute;top:33.74%; left:8.6%;width:13.77%;height:20.67%'> <div class=O style='position:absolute;top:36.39%;left:18.41%;width:1.72%; height:11.48%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:49.23%;left:7.69%;width:84.61%; height:50.76%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <div class=O style='position:absolute;top:36.04%;left:10.99%;width:1.72%; height:11.48%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:46.15%'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:49.23%;left:7.69%;width:84.61%; height:50.76%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <div class=O style='position:absolute;top:37.8%;left:20.66%;width:.13%; height:12.01%'> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:0%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; display:none'><b><br> </b></span></div> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17;position:absolute;top:51.47%;left:0%;width:100.0%; height:48.52%'><span style='font-family:Palatino;font-size:233%;color:white; mso-special-format:lastCR;display:none'><b><br> </b></span></div> </div> <img border=0 src="slide0003_image062.png" style='position:absolute;top:27.38%; left:4.9%;width:21.45%;height:21.37%'> <div style='position:absolute;top:27.38%;left:5.03%;width:20.92%;height:12.54%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:5.63%;left:6.32%;width:94.3%; height:87.32%'> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:50.0%'><span style='font-size:200%;color:#E9EB5D'><i>trans QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:48.38%;left:0%;width:83.22%;height:50.0%'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This slide is illustrates two major types of QTLs that modulate variability in transcript-relative steady state abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers or may be in 3Õ UTR binding sites that affect message stability.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be fairly certain that the QTL is not in the gene itself. The most blatant type of trans QTL would be a polymorphism in a transcription factor. But in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlapping arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> 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face=Helvetica size=2>This slide is illustrates two major types of QTLs that modulate variability in transcript-relative steady state abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers or may be in 3Õ UTR binding sites that affect message stability.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be fairly certain that the QTL is not in the gene itself. The most blatant type of trans QTL would be a polymorphism in a transcription factor. But in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlapping arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004.htm deleted file mode 100755 index 8f72f910..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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: Discovering upstream modulatory loci"> <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.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0004_image063.png" style='position:absolute;top:38.86%; left:5.03%;width:84.9%;height:45.75%'> <div style='position:absolute;top:5.47%;left:2.51%;width:93.64%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";position:absolute;top:20.4%; left:1.41%;width:97.31%;height:75.51%'><span style='font-family:Verdana; font-size:64%'>Discovering upstream modulatory loci</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </div> <img border=0 src="slide0004_image064.png" style='position:absolute;top:20.31%; left:18.01%;width:19.2%;height:25.97%'><img border=0 src="slide0004_image065.png" style='position:absolute;top:32.5%;left:78.01%; width:19.2%;height:25.97%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image010.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image010.png deleted file mode 100755 index 08c136e3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image010.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image012.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image012.png deleted file mode 100755 index b8e67f4d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image012.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image063.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image063.png deleted file mode 100755 index 891bc06c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image063.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image064.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image064.png deleted file mode 100755 index 8905caa6..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image064.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image065.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image065.png deleted file mode 100755 index 7f5a5295..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_image065.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_notes_pane.htm deleted file mode 100755 index b1988954..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0004_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </body> </html> \ 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 deleted file mode 100755 index b2dc8582..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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: 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><!-- -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%'> <div style='position:absolute;top:-.53%;left:1.72%;width:101.19%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:98.95%; height:75.51%'><span style='font-family:Verdana;font-size:64%'><i>WebQTL searches for upstream controllers</i></span><span style='font-family:Verdana; font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> <div style='position:absolute;top:71.02%;left:34.96%;width:45.96%;height:19.78%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:3.57%;left:2.3%;width:97.69%; height:91.96%'><span style='position:absolute;top:0%;left:0%;width:98.82%'><span style='font-size:167%;color:#E9EB5D'><i>App maps on Chr 16 (blue </i></span></span><span style='position:absolute;top:25.24%;left:0%;width:100.0%'><span style='font-size:167%;color:#E9EB5D'><i>arrow points to the orange </i></span></span><span style='position:absolute;top:49.51%;left:0%;width:86.72%'><span style='font-size:167%;color:#E9EB5D'><i>triangle) but the best </i></span></span><span style='position:absolute;top:74.75%;left:0%;width:86.72%'><span style='font-size:167%;color:#E9EB5D'><i>locus is on Chr 7.</i></span><span style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> </div> <img border=0 src="slide0005_image066.png" style='position:absolute;top:8.83%; left:1.19%;width:98.27%;height:53.88%'><img border=0 src="slide0005_image067.png" style='position:absolute;top:46.64%;left:15.76%; width:15.89%;height:53.35%'><img border=0 src="slide0005_image068.png" style='position:absolute;top:46.64%;left:80.0%;width:10.99%;height:53.35%'><img border=0 src="slide0005_image069.png" style='position:absolute;top:41.34%; left:76.02%;width:11.65%;height:22.79%'><img border=0 src="slide0005_image070.png" style='position:absolute;top:41.51%;left:29.13%; width:12.71%;height:24.38%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The red line and the red axis to the far right provide an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>6. You can also download the results of the analysis in a text format</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image013.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image013.png deleted file mode 100755 index 55769e36..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image013.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image014.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image014.png deleted file mode 100755 index e49ba16e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image014.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image066.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image066.png deleted file mode 100755 index 5ab7794c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image066.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image067.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image067.png deleted file mode 100755 index c26d4792..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image067.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image068.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image068.png deleted file mode 100755 index af0745a5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image068.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image069.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image069.png deleted file mode 100755 index 6ec88720..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image069.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image070.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image070.png deleted file mode 100755 index 9c156ddc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_image070.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_notes_pane.htm deleted file mode 100755 index 279e38cf..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0005_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The red line and the red axis to the far right provide an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>6. You can also download the results of the analysis in a text format</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006.htm deleted file mode 100755 index f647c55a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <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: 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><!-- -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:-.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><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image015.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image015.png deleted file mode 100755 index ff7d776a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image015.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image071.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image071.png deleted file mode 100755 index 0e63f836..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image071.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image072.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image072.png deleted file mode 100755 index 3c44c2ab..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_image072.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_notes_pane.htm deleted file mode 100755 index c1f7d244..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0006_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <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>The map on the top has an X-axis scale based on frequency of recombinations events between markers (B to D transitions, see slide 19 for a color-coded example). These so-called genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast, the physical map shown below the genetic map has an X-axis scale based on DNA length measured in nucleotides or base-pairs. Notice the large difference between the two maps in the size of Chr 19 (large on the genetic scale but small on the physical scale).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Also notice the large difference in the width of the chromosome 7 QTL peak. In mice, recombinations occur with higher frequency toward the telomeric side (right side) of each chromosome. As a result, genetic maps are stretched out more toward the telomere relative to a physical map. The QTL on distal Chr 7 is therefore actually more precisely mapped than might appear looking at the genetic map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The physical scale is becoming more useful than the genetic scale primarily because many other data types can be easily superimposed on a physical map. You will see more examples in the next several slides.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007.htm deleted file mode 100755 index 01fb76a9..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <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: Physical map for distal chromosome 7"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- -gId="slide0007.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//--> -</script><script for=window event=onload language=JavaScript><!-- -if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//--> -</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.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"> </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><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image016.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image016.png deleted file mode 100755 index 53a17c76..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image016.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image017.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image017.png deleted file mode 100755 index 308c4df0..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image017.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image073.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image073.png deleted file mode 100755 index c0174c3f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image073.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image075.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image075.png deleted file mode 100755 index 9a3e3264..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_image075.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_notes_pane.htm deleted file mode 100755 index 24c42724..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0007_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <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 SNPs have closely matched sequences and are less likely to contain QTLs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4. As before, the thin red line shows the additive effect size. By convention the positive values signify the D alleles are associated with higher expression of App in this region of Chr 7 than the B alleles. The maximum effect size is about +0.20 log2 expression units per D allele. The differences been the BB and DD genotypes (BB and DD because each strain has two alleles; one per chromosome) is therefore about 2^0.4 = 1.32 or a 32% increment in DD relative to BB at this locus.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5. If you scroll just under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps are zoomable, a feature we will exploit to evaluate candidate genes in this QTL interval.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008.htm deleted file mode 100755 index 8a9290b6..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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: Evaluating candidate genes"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- -gId="slide0008.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//--> -</script><script for=window event=onload language=JavaScript><!-- -if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//--> -</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><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"> </span></i></span><span style='font-size:200%; color:#E9EB5D'><i>= better<br> </i></span></div> <div style='text-align:center;position:absolute;top:56.94%;left:0%;width:100.0%; height:43.05%'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></span></div> </div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QTL gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <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/slide0008_image018.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image018.png deleted file mode 100755 index 9535e6bb..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image018.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image019.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image019.png deleted file mode 100755 index 7e86d735..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image019.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image021.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image021.png deleted file mode 100755 index 2f8dfb0a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image021.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image076.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image076.png deleted file mode 100755 index 14e3fbe5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image076.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image077.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image077.png deleted file mode 100755 index ec9fff87..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_image077.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_notes_pane.htm deleted file mode 100755 index 9f5e373a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0008_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QTL gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009.htm deleted file mode 100755 index 16351b5b..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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: Physical maps are zoomable"> <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.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"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </div> <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/slide0009_image022.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image022.png deleted file mode 100755 index e03c35ed..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image022.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image078.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image078.png deleted file mode 100755 index 93d21c90..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image078.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image079.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image079.png deleted file mode 100755 index fdc27d23..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image079.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image080.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image080.png deleted file mode 100755 index d2cb5ee3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_image080.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_notes_pane.htm deleted file mode 100755 index 39c42e72..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0009_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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>An even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010.htm deleted file mode 100755 index 91cf9f00..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <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: Evaluating Ctbp2 as a candidate QTL for 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><!-- -gId="slide0010.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:1.72%;width:106.35%;height:7.24%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:12.19%;left:.87%;width:99.12%; height:90.24%'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span style='font-family:Verdana;font-size:64%'> as a candidate QTL for </span><span style='font-family:Verdana;font-size:64%'><i>App</i></span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </div> <img border=0 src="slide0010_image082.png" style='position:absolute;top:94.52%; left:3.31%;width:96.68%;height:4.24%'><img border=0 src="slide0010_image083.png" style='position:absolute;top:7.77%;left:3.31%;width:48.34%;height:40.28%'> <div class=O style='position:absolute;top:52.82%;left:55.23%;width:35.76%; height:37.98%'><span style='position:absolute;top:0%;left:0%;width:94.81%'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%; color:#E9EB5D'><i> the </i></span></span><span style='position:absolute; top:16.74%;left:0%;width:95.92%'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2 </i></span><span style='font-size:233%;color:#E9EB5D'>cis QTL, </span></span><span style='position:absolute;top:33.48%;left:0%;width:98.14%'><span style='font-size:233%;color:#E9EB5D'>but is detected </span></span><span style='position:absolute;top:49.76%;left:0%;width:94.81%'><span style='font-size:233%;color:#E9EB5D'>only in the </span></span><span style='position:absolute;top:66.51%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'>Rosen striatum </span></span><span style='position:absolute;top:83.25%;left:0%;width:94.81%'><span style='font-size:233%;color:#E9EB5D'>data set.</span><span style='font-size: 233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></div> <div class=O style='position:absolute;top:16.25%;left:56.02%;width:48.21%; height:12.72%'><span style='position:absolute;top:0%;left:0%;width:94.78%'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%; color:#E9EB5D'><i> the App QTL </i></span></span><span style='position:absolute; top:48.61%;left:0%;width:100.0%'><span style='font-size:233%;color:#E9EB5D'>in the INIA data set. </span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></div> <img border=0 src="slide0010_image084.png" style='position:absolute;top:39.39%; left:3.31%;width:48.47%;height:53.35%'><img border=0 src="slide0010_image085.png" style='position:absolute;top:10.95%;left:35.36%; width:.39%;height:72.79%'><img border=0 src="slide0010_image086.png" style='position:absolute;top:10.95%;left:31.52%;width:.39%;height:72.79%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differences may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consistency of QTL peaks.</font><br> </td> </tr> </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/slide0010_image023.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image023.png deleted file mode 100755 index 1d32d035..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image023.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image024.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image024.png deleted file mode 100755 index 152e5045..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image024.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image082.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image082.png deleted file mode 100755 index cf5f70f7..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image082.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image083.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image083.png deleted file mode 100755 index a5886d21..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image083.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image084.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image084.png deleted file mode 100755 index 7eb77319..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image084.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image085.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image085.png deleted file mode 100755 index 99f4d04d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image085.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image086.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image086.png deleted file mode 100755 index ac87ce02..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_image086.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_notes_pane.htm deleted file mode 100755 index bdb257fb..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0010_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differences may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana size=2> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consistency of QTL peaks.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011.htm deleted file mode 100755 index dd8304f8..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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: Evaluating Ctbp2 using other resources"> <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:0%;left:1.72%;width:101.05%;height:8.65%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;position:absolute;top:18.36%;left:.91%;width:97.9%; height:75.51%'><span style='font-family:Verdana;font-size:64%'>Evaluating </span><span style='font-family:Verdana;font-size:64%'><i>Ctbp2</i></span><span style='font-family:Verdana;font-size:64%'> using other resources</span><span style='font-family:Verdana;font-size:73%;mso-special-format:lastCR;display: none'><i><br> </i></span></div> </div> <img border=0 src="slide0011_image087.png" style='position:absolute;top:10.07%; left:1.72%;width:48.21%;height:53.35%'><img border=0 src="slide0011_image088.png" style='position:absolute;top:40.81%;left:19.2%; width:78.54%;height:54.77%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The C-terminal binding protein 2 is a transcriptional co-repressor also known as Ribeye.</font><font face=Times-Roman size=3> The gene produces two transcripts encoding distinct proteins. The short form is a transcriptional repressor that binds a Pro-X-Asp-Leu-Ser peptide motif and interacts with several transcription factors including EVI1, ZFPM1, and ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component of specialized synapses in photoreceptors. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. To find out more about CTBP2 protein and the Ctbp2 gene, link to iHOP at http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Try Arrowsmith at http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Both APP and CTBP2 are involved in oxidoreducatase activity or Notch signaling. To establish this common gene ontology visit NCBI<span style="mso-spacerun: yes"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. You can get interesting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particular interest with respect to APP protein processing, Ctbp2 covaries positively with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <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/slide0011_image025.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image025.png deleted file mode 100755 index d29a333f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image025.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image087.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image087.png deleted file mode 100755 index a6ca39ae..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image087.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image088.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image088.png deleted file mode 100755 index c17a41bc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_image088.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_notes_pane.htm deleted file mode 100755 index c287e06e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0011_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The C-terminal binding protein 2 is a transcriptional co-repressor also known as Ribeye.</font><font face=Times-Roman size=2> The gene produces two transcripts encoding distinct proteins. The short form is a transcriptional repressor that binds a Pro-X-Asp-Leu-Ser peptide motif and interacts with several transcription factors including EVI1, ZFPM1, and ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component of specialized synapses in photoreceptors. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. To find out more about CTBP2 protein and the Ctbp2 gene, link to iHOP at http://www.pdg.cnb.uam.es/UniPub/iHOP/ and type in CTBP2</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Try Arrowsmith at http://arrowsmith.psych.uic.edu/cgi-test/arrowsmith_uic/pubsmith.cgi</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. Both APP and CTBP2 are involved in oxidoreducatase activity or Notch signaling. To establish this common gene ontology visit NCBI<span style="mso-spacerun: yes"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. You can get interesting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particular interest with respect to APP protein processing, Ctbp2 covaries positively with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012.htm deleted file mode 100755 index 852e722e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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="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:3.31%;width:93.64%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292; mso-text-indent-alt:0;position:absolute;top:0%;left:1.13%;width:97.59%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 2</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div style='position:absolute;top:15.01%;left:5.96%;width:101.19%;height:31.09%'> <div class=O1 style='mso-margin-left-alt:432'></div> <div class=O2 style='mso-margin-left-alt:720'></div> <div class=O3 style='mso-margin-left-alt:1008'></div> <div class=O4 style='mso-margin-left-alt:1296'></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:0%; left:0%;width:86.25%;height:14.2%'><span style='position:absolute;top:0%; left:2.88%;width:97.11%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.96%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Covered the basics of QTL analysis and mapping.<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:14.2%; left:0%;width:86.25%;height:14.2%'><span style='position:absolute;top:0%; left:2.88%;width:97.11%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.96%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Reviewed difference between genetic and physical maps.<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:28.4%; left:0%;width:100.0%;height:42.61%'><span style='position:absolute;top:0%; left:2.48%;width:97.51%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.55%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed interpreting features of QTL maps including the LRS function, </span></span><span style='position: absolute;top:33.33%;left:2.48%;width:91.23%'><span style='font-family:"Gill Sans"; font-size:167%;color:#E9EB5D;mso-color-index:3'>the additive effect function, the bootstrap bars, and the permutation </span></span><span style='position: absolute;top:68.0%;left:2.48%;width:83.76%'><span style='font-family:"Gill Sans"; font-size:167%;color:#E9EB5D;mso-color-index:3'>thresholds.<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:71.59%; left:0%;width:88.35%;height:14.2%'><span style='position:absolute;top:0%; left:2.81%;width:97.18%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.89%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Illustrated techniques to generate a list of positional candidates.<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:85.79%; left:0%;width:86.25%;height:14.2%'><span style='position:absolute;top:0%; left:2.88%;width:97.11%'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.96%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed some factors used to evaluate candidate genes.</span></span></div> </div> <div class=O style='position:absolute;top:58.65%;left:5.96%;width:106.22%; height:22.26%'><span style='position:absolute;top:0%;left:0%;width:84.53%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>What does a QTL signify? A good QTL is a claim that a particular </span></span><span style='position:absolute;top:19.84%;left:0%;width:96.38%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>chromosomal region contains a causal source of variation in the phenotype. </span></span><span style='position:absolute;top:39.68%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>The importance of this hypothesis depends on the quality and relevance of the </span></span><span style='position:absolute;top:59.52%;left:0%;width:90.89%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>phenotype and the statistical strength of the QTL. As usual, test and be </span></span><span style='position:absolute;top:79.36%;left:0%;width:84.53%'><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'>skeptical.</span></span></div> </div> <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/slide0012_image026.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_image026.png deleted file mode 100755 index a0675ffc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_image026.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_notes_pane.htm deleted file mode 100755 index 895ab29b..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0012_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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>By clicking on the CORRELATION of the Atcay transcript to the App transcript, you can generate a Correlation plot between these two transcripts. In this App and Atcay scatterplot, each point is a strain mean value. For example, BXD33 and BXD8 have low App and Atcay expressions. The two parental strains and the F1 are also included in this plot.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013.htm deleted file mode 100755 index f8993810..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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: 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" -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: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><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_image027.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_image027.png deleted file mode 100755 index ba473846..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_image027.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_notes_pane.htm deleted file mode 100755 index 190b8653..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0013_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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 diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014.htm deleted file mode 100755 index e5de4030..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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: 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="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: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><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image029.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image029.png deleted file mode 100755 index 8f560834..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image029.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image031.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image031.png deleted file mode 100755 index 8d72b4c1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image031.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image033.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image033.png deleted file mode 100755 index c1cd1c01..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_image033.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_notes_pane.htm deleted file mode 100755 index 4a9d3b57..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0014_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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>END</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015.htm deleted file mode 100755 index 89e5d8e5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015.htm +++ /dev/null @@ -1,155 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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"> <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("slide0015.htm"); -}//--> -</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> - -g_origHeight = 566; -g_origWidth = 755; 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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 = 0.03 * g_height; myleft = 0.02 * 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><script> - mytop = 0.02 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:73%'>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes"> </span><br> </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 0.89 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:73%'>link to www.genenetwork.org</span><span style='font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> - mytop = 0.24 * g_height; myleft = 0.05 * g_width; myheight = 0.68 * g_height; mywidth = 0.54 * 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 = 0.42 * g_height; mywidth = 0.52 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.21 * g_height; mywidth = 0.52 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.46 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 1. How to study </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>expression variation </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.47 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>and genetic correlation </span></span></layer><script> - mytop = 0.15 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 2–17)<br> </span></span></layer></div> </layer><script> - mytop = 0.25 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.46 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.43 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>upstream modulators </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 18–29)</span></span></layer></div> </layer></div> </layer></div> </layer><script> - mytop = 0.17 * g_height; myleft = 0.74 * g_width; myheight = 0.64 * g_height; mywidth = 0.23 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.74 * g_width; -yy = 0.17 * g_height; -ht = 0.64 * g_height; -wd = 0.23 * g_width; -document.write( -'<img border=0 src="slide0001_image001.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.75 * g_height; myleft = 0.74 * g_width; myheight = 0.14 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> </layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </layer></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 = 0.5 * g_height; myleft = 0.48 * g_width; myheight = 0.13 * g_height; mywidth = 0.25 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.48 * g_width; -yy = 0.5 * g_height; -ht = 0.13 * g_height; -wd = 0.25 * g_width; -document.write( -'<img border=0 src="slide0001_image002.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>Part 2: Discovering upstream modulators and quantitative trait loci (QTLs). A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</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/slide0015_image034.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image034.png deleted file mode 100755 index dafa2898..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image034.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image035.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image035.png deleted file mode 100755 index 35566d47..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_image035.png +++ /dev/null Binary files differdiff --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 deleted file mode 100755 index c4c4ec6d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0015_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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>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.ppt_files/slide0016.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016.htm deleted file mode 100755 index ea69ff33..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016.htm +++ /dev/null @@ -1,919 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.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: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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- -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="master05_background.png" height=' + ht + ' width=' + wd + '>' ); 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-</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="slide0002_image003.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.2 * g_height; myleft = 0.28 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.28 * g_width; -yy = 0.2 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image004.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.15 * g_height; myleft = 0.25 * g_width; myheight = 0.09 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>C57BL/6J (B)<br> </span></div> </layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.2 * g_height; myleft = 0.3 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.3 * g_width; -yy = 0.2 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image005.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.15 * g_height; myleft = 0.62 * g_width; myheight = 0.09 * g_height; mywidth = 0.16 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>DBA/2J (D)<br> </span></div> </layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.2 * g_height; myleft = 0.66 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.66 * g_width; -yy = 0.2 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image006.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.35 * g_height; myleft = 0.23 * g_width; myheight = 0.01 * g_height; mywidth = 0.5 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.23 * g_width; -yy = 0.35 * g_height; -ht = 0.01 * g_height; -wd = 0.5 * g_width; -document.write( -'<img border=0 src="slide0002_image007.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.35 * g_height; myleft = 0.24 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.24 * g_width; -yy = 0.35 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image008.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.35 * g_height; myleft = 0.4 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.4 * g_width; -yy = 0.35 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image009.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.35 * g_height; myleft = 0.57 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.57 * g_width; -yy = 0.35 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image010.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.35 * g_height; myleft = 0.74 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.74 * g_width; -yy = 0.35 * g_height; -ht = 0.03 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image011.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.42 * g_height; myleft = 0.05 * g_width; myheight = 0.12 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F1<br> </b></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format: lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.39 * g_height; myleft = 0.22 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.22 * g_width; -yy = 0.39 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image012.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.39 * g_height; myleft = 0.38 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.38 * g_width; -yy = 0.39 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image013.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.39 * g_height; myleft = 0.55 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.55 * g_width; -yy = 0.39 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image014.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.39 * g_height; myleft = 0.72 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.72 * g_width; -yy = 0.39 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image015.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.43 * g_height; myleft = 0.43 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.43 * g_width; -yy = 0.43 * g_height; -ht = 0.03 * g_height; -wd = 0.11 * g_width; -document.write( -'<img border=0 src="slide0002_image016.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.6 * g_height; myleft = 0.2 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.2 * g_width; -yy = 0.6 * g_height; -ht = 0.03 * g_height; -wd = 0.09 * g_width; -document.write( -'<img border=0 src="slide0002_image017.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.71 * g_height; myleft = 0.58 * g_width; myheight = 0.26 * g_height; mywidth = 0.2 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0.03 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>20 generations </b></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>brother-sister </b></span></span></layer><script> - mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:center'><span style='font-family:Arial;font-size:117%; color:#FFFF99'><b>matings</b></span><span style='font-family:Arial;font-size: 233%;color:#FFFF99;display:none'><b><br> </b></span></span></layer></div> </layer><script> - mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:233%; color:#FFFF99;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.6 * g_height; myleft = 0.5 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.5 * g_width; -yy = 0.6 * g_height; -ht = 0.03 * g_height; -wd = 0.09 * g_width; -document.write( -'<img border=0 src="slide0002_image018.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.62 * g_height; myleft = 0.54 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.54 * g_width; -yy = 0.62 * g_height; -ht = 0.28 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image019.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.61 * g_height; myleft = 0.79 * g_width; myheight = 0.03 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.79 * g_width; -yy = 0.61 * g_height; -ht = 0.03 * g_height; -wd = 0.1 * g_width; -document.write( -'<img border=0 src="slide0002_image020.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.62 * g_height; myleft = 0.83 * g_width; myheight = 0.28 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.83 * g_width; -yy = 0.62 * g_height; -ht = 0.28 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image021.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.92 * g_height; myleft = 0.21 * g_width; myheight = 0.09 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD1</span><span style='font-family:Arial;font-size:150%;color:#484848;display:none'><br> </span></div> </layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#484848;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.92 * g_height; myleft = 0.51 * g_width; myheight = 0.09 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>BXD2<br> </span></div> </layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.92 * g_height; myleft = 0.8 * g_width; myheight = 0.05 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-173 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-173 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>BXD80</span></div> </layer></div> </layer><script> - mytop = 0.9 * g_height; myleft = 0.64 * g_width; myheight = 0.17 * g_height; mywidth = 0.17 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.15 * g_height; mywidth = 0.16 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.16 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:300%;color:#FFFF99'>+ É +<br> </span></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-341 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:300%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.62 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99'><b>F2<br> </b></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-230 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:200%;color:#FFFF99;mso-special-format: lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.54 * g_height; myleft = 0.18 * g_width; myheight = 0.01 * g_height; mywidth = 0.75 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.18 * g_width; -yy = 0.54 * g_height; -ht = 0.01 * g_height; -wd = 0.75 * g_width; -document.write( -'<img border=0 src="slide0002_image022.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.54 * g_height; myleft = 0.17 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.17 * g_width; -yy = 0.54 * g_height; -ht = 0.03 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image023.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.54 * g_height; myleft = 0.32 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.32 * g_width; -yy = 0.54 * g_height; -ht = 0.03 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image024.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.54 * g_height; myleft = 0.48 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.48 * g_width; -yy = 0.54 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image025.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.54 * g_height; myleft = 0.62 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.62 * g_width; -yy = 0.54 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image026.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.54 * g_height; myleft = 0.77 * g_width; myheight = 0.04 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.77 * g_width; -yy = 0.54 * g_height; -ht = 0.04 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image027.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.54 * g_height; myleft = 0.92 * g_width; myheight = 0.03 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.92 * g_width; -yy = 0.54 * g_height; -ht = 0.03 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image028.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.44 * g_height; myleft = 0.49 * g_width; myheight = 0.1 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.49 * g_width; -yy = 0.44 * g_height; -ht = 0.1 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0002_image029.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.57 * g_height; myleft = 0.15 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.15 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image030.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.57 * g_height; myleft = 0.3 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.3 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image031.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.57 * g_height; myleft = 0.46 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.46 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image032.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.57 * g_height; myleft = 0.6 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.6 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image033.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.75 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image034.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.57 * g_height; myleft = 0.9 * g_width; myheight = 0.11 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.9 * g_width; -yy = 0.57 * g_height; -ht = 0.11 * g_height; -wd = 0.04 * g_width; -document.write( -'<img border=0 src="slide0002_image035.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.84 * g_height; myleft = 0.56 * g_width; myheight = 0.01 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.56 * g_width; -yy = 0.84 * g_height; -ht = 0.01 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image036.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.8 * g_height; myleft = 0.25 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.25 * g_width; -yy = 0.8 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image037.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.84 * g_height; myleft = 0.86 * g_width; myheight = 0.02 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.86 * g_width; -yy = 0.84 * g_height; -ht = 0.02 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image038.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.75 * g_height; myleft = 0.01 * g_width; myheight = 0.13 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'><b>BXD RI<br> </b></span></div> </layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'><b>Strain set<br> </b></span></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0.01 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.12 * g_height; myleft = 0.14 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.14 * g_width; -yy = 0.12 * g_height; -ht = 0.06 * g_height; -wd = 0.1 * g_width; -document.write( -'<img border=0 src="slide0002_image039.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.76 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.76 * g_width; -yy = 0.1 * g_height; -ht = 0.08 * g_height; -wd = 0.14 * g_width; -document.write( -'<img border=0 src="slide0002_image040.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.2 * g_height; myleft = 0.17 * g_width; myheight = 0.13 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>fully<br> </span></div> </layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>inbred<br> </span></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.38 * g_height; myleft = 0.02 * g_width; myheight = 0.09 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>isogenic<br> </span></div> </layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.54 * g_height; myleft = 0.01 * g_width; myheight = 0.13 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.11 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>hetero-<br> </span></div> </layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>geneous<br> </span></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.74 * g_height; myleft = 0.29 * g_width; myheight = 0.21 * g_height; mywidth = 0.21 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.19 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>Recombined </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>chromosomes </span></span></layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>are needed for </span></span></layer><script> - mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:center'><span style='font-family:Arial;font-size:150%; color:#FFFF99'>mapping<br> </span></span></layer></div> </layer><script> - mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-173 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:150%; color:#FFFF99;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.25 * g_width; myheight = 0.09 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>female<br> </span></div> </layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.64 * g_width; myheight = 0.09 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99'>male<br> </span></div> </layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.05 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.3 * g_height; myleft = 0.78 * g_width; myheight = 0.09 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0.01 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:117%;color:#FFFF99'>chromosome pair</span><span style='font-family:Arial;font-size:150%;color:#FFFF99; display:none'><br> </span></div> </layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-173 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:Arial;font-size:150%;color:#FFFF99;mso-special-format: lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.31 * g_height; myleft = 0.65 * g_width; myheight = 0.02 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.65 * g_width; -yy = 0.31 * g_height; -ht = 0.02 * g_height; -wd = 0.12 * g_width; -document.write( -'<img border=0 src="slide0002_image041.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.86 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.12 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>Inbred<br> </span></div> </layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>Isogenic<br> </span></div> </layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:#E9EB5D'>siblings</span><span style='font-family:Arial;font-size:117%; color:aqua;display:none'><br> </span></div> </layer><script> - mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-134 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Arial;font-size:117%; color:aqua;mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.79 * g_height; myleft = 0.83 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.83 * g_width; -yy = 0.79 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image042.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.84 * g_height; myleft = 0.83 * g_width; myheight = 0.02 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.83 * g_width; -yy = 0.84 * g_height; -ht = 0.02 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image043.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.79 * g_height; myleft = 0.53 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.53 * g_width; -yy = 0.79 * g_height; -ht = 0.11 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image044.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.83 * g_height; 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myleft = 0.63 * g_width; myheight = 0.08 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.63 * g_width; -yy = 0.61 * g_height; -ht = 0.08 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0002_image053.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>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. Over the last decade, our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD strains. They have all been genotyped using about 13,700 markers (SNPs and microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ regions of the chromosomes as shown in the figure above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Chromosomes of RI GRPs usually have about 4 times as many recombinations as those of F2 animals. However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50 RI strains contain as many recombinations as 100 F2 animals.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. BXD43 through BXD100 were generated using a special method that resulted in a further doubling of the average recombination density per chromosome. The entire set of 80 BXDs therefore contains as many recombinations as about 260 F2 animals.</font><br> </td> </tr> </table> </div> </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/slide0016_image036.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_image036.png deleted file mode 100755 index baa1d807..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_image036.png +++ /dev/null Binary files differdiff --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 deleted file mode 100755 index f5776dad..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0016_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.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>We have computed the Network Graph, now using other types of traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Saline Hot Plate Latency is the green node labeled 10020.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Freezing (fear) is the green node labeled 10447.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0017.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0017.htm deleted file mode 100755 index cc8ff93a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0017.htm +++ /dev/null @@ -1,421 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); 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-</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:"-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 + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.71 * g_height; myleft = 0.07 * g_width; myheight = 0.12 * g_height; mywidth = 0.16 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.57 * g_height; myleft = -0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = -0.01 * g_width; -yy = 0.57 * g_height; -ht = 0.07 * g_height; -wd = 1.01 * g_width; -document.write( -'<img border=0 src="slide0003_image059.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.44 * g_height; myleft = 0.47 * g_width; myheight = 0.12 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69'>Low<br> </span></div> </layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> - mytop = 0.58 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.04 * g_height; mywidth = 1.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Gadget;font-size:167%; color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR >>>>></span></div> </layer></div> </layer><script> - mytop = 0.37 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.08 * g_width; -yy = 0.37 * g_height; -ht = 0.2 * g_height; -wd = 0.13 * g_width; -document.write( -'<img border=0 src="slide0003_image060.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.4 * g_height; myleft = 0.1 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> - mytop = 0.4 * g_height; myleft = 0.18 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> - mytop = 0.33 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.08 * g_width; -yy = 0.33 * g_height; -ht = 0.2 * g_height; -wd = 0.13 * g_width; -document.write( -'<img border=0 src="slide0003_image061.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.36 * g_height; myleft = 0.18 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> - mytop = 0.36 * g_height; myleft = 0.1 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </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:"-269 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:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> - mytop = 0.27 * 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="slide0003_image062.png" 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 = 0.2 * 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> - 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:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer></div> </LAYER> - <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"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018.htm deleted file mode 100755 index a2c8a7db..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018.htm +++ /dev/null @@ -1,115 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: Discovering upstream modulatory loci"> <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("slide0018.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.38 * g_height; myleft = 0.05 * g_width; myheight = 0.45 * g_height; mywidth = 0.84 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.05 * g_width; -yy = 0.38 * g_height; -ht = 0.45 * g_height; -wd = 0.84 * g_width; -document.write( -'<img border=0 src="slide0004_image063.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.08 * g_height; mywidth = 0.93 * 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 = 0.91 * 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> - mytop = 0.2 * g_height; myleft = 0.18 * g_width; myheight = 0.25 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.18 * g_width; -yy = 0.2 * g_height; -ht = 0.25 * g_height; -wd = 0.19 * g_width; -document.write( -'<img border=0 src="slide0004_image064.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.32 * g_height; myleft = 0.78 * g_width; myheight = 0.25 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.78 * g_width; -yy = 0.32 * g_height; -ht = 0.25 * g_height; -wd = 0.19 * g_width; -document.write( -'<img border=0 src="slide0004_image065.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>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image037.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image037.png deleted file mode 100755 index a1cb20e4..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image037.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image038.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image038.png deleted file mode 100755 index e06bd0db..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_image038.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_notes_pane.htm deleted file mode 100755 index 9e0445f3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0018_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 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/slide0019.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019.htm deleted file mode 100755 index 43fc12fd..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0019.htm +++ /dev/null @@ -1,155 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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: WebQTL searches for upstream controllers"> <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("slide0019.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.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 = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>WebQTL searches for upstream controllers</i></span><span style='font-family:Verdana; font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> - mytop = 0.71 * g_height; myleft = 0.34 * g_width; myheight = 0.19 * g_height; mywidth = 0.45 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.18 * g_height; mywidth = 0.44 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.44 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>App maps on Chr 16 (blue </i></span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.44 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>arrow points to the orange </i></span></span></layer><script> - mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.38 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>triangle) but the best </i></span></span></layer><script> - mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.38 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>locus is on Chr 7.</i></span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.53 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.08 * g_height; -ht = 0.53 * g_height; -wd = 0.98 * g_width; -document.write( -'<img border=0 src="slide0005_image066.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.46 * g_height; myleft = 0.15 * g_width; myheight = 0.53 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.15 * g_width; -yy = 0.46 * g_height; -ht = 0.53 * g_height; -wd = 0.15 * g_width; -document.write( -'<img border=0 src="slide0005_image067.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.46 * g_height; myleft = 0.8 * g_width; myheight = 0.53 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.8 * g_width; -yy = 0.46 * g_height; -ht = 0.53 * g_height; -wd = 0.1 * g_width; -document.write( -'<img border=0 src="slide0005_image068.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.41 * g_height; myleft = 0.76 * g_width; myheight = 0.22 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.76 * g_width; -yy = 0.41 * g_height; -ht = 0.22 * g_height; -wd = 0.11 * g_width; -document.write( -'<img border=0 src="slide0005_image069.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.41 * g_height; myleft = 0.29 * g_width; myheight = 0.24 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.29 * g_width; -yy = 0.41 * g_height; -ht = 0.24 * g_height; -wd = 0.12 * g_width; -document.write( -'<img border=0 src="slide0005_image070.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>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The red line and the red axis to the far right provide an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>6. 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<tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <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 diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020.htm deleted file mode 100755 index d148b0c8..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020.htm +++ /dev/null @@ -1,113 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: Genetic versus Physical maps for App expression"> <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("slide0020.htm"); -}//--> -</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> - -g_origHeight = 566; -g_origWidth = 755; 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mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>Genetic versus Physical maps for App expression</i></span><span style='font-family: Verdana;font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.39 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.08 * g_height; -ht = 0.39 * g_height; -wd = 0.98 * g_width; -document.write( -'<img border=0 src="slide0006_image071.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.35 * g_height; myleft = 0.01 * g_width; myheight = 0.54 * g_height; mywidth = 0.98 * 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-size:117%;color:#E9EB5D'><i>The difference between genetic and physical scale is analogous to measuring the </i></span></span></layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>separation between New York and Boston in either travel hours or kilometers</i></span><span style='font-size:150%;color:#E9EB5D'><i>.</i></span><span style='font-size: 167%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </LAYER> - <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The map on the top has an X-axis scale based on frequency of recombinations events between markers (B to D transitions, see slide 19 for a color-coded example). These so-called genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast, the physical map shown below the genetic map has an X-axis scale based on DNA length measured in nucleotides or base-pairs. Notice the large difference between the two maps in the size of Chr 19 (large on the genetic scale but small on the physical scale).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Also notice the large difference in the width of the chromosome 7 QTL peak. In mice, recombinations occur with higher frequency toward the telomeric side (right side) of each chromosome. As a result, genetic maps are stretched out more toward the telomere relative to a physical map. The QTL on distal Chr 7 is therefore actually more precisely mapped than might appear looking at the genetic map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The physical scale is becoming more useful than the genetic scale primarily because many other data types can be easily superimposed on a physical map. You will see more examples in the next several slides.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image090.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image090.png deleted file mode 100755 index 3f7c7606..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image090.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image091.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image091.png deleted file mode 100755 index 3f7c7606..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image091.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image092.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image092.png deleted file mode 100755 index 272f8318..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image092.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image093.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image093.png deleted file mode 100755 index a526d207..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image093.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image094.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image094.png deleted file mode 100755 index 7a08eae6..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image094.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image095.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image095.png deleted file mode 100755 index f2e33d2d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image095.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image096.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image096.png deleted file mode 100755 index 2c8ab141..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image096.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image097.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image097.png deleted file mode 100755 index 9665dc0f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image097.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image098.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image098.png deleted file mode 100755 index 4c8023d2..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_image098.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_notes_pane.htm deleted file mode 100755 index 68c0fb55..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0020_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>This slide is illustrates two major types of QTLs that modulate variability in transcript-relative steady state abundance.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers or may be in 3Õ UTR binding sites that affect message stability.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be fairly certain that the QTL is not in the gene itself. The most blatant type of trans QTL would be a polymorphism in a transcription factor. But in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlapping arrows in the figure.<span style="mso-spacerun: yes"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm deleted file mode 100755 index c7854145..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021.htm +++ /dev/null @@ -1,110 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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: 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> -<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("slide0021.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.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> - 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> - mytop = 0.93 * g_height; myleft = 0.06 * g_width; myheight = 0.03 * g_height; mywidth = 0.75 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.06 * g_width; -yy = 0.93 * g_height; -ht = 0.03 * g_height; -wd = 0.75 * g_width; -document.write( -'<img border=0 src="slide0007_image073.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.15 * g_height; myleft = 0.06 * g_width; myheight = 0.75 * g_height; mywidth = 0.68 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.06 * g_width; -yy = 0.15 * g_height; -ht = 0.75 * g_height; -wd = 0.68 * g_width; -document.write( -'<img border=0 src="slide0007_image075.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>Physical map of variation in App expression in brain on distal Chr 7 (a blow up of the whole-genome map on the previous slide).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> You can now see that the X-axis is on a physical scale of megabases (Mb). The QTL peak is roughly between 120 and 132 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The small irregular colored blocks and marks toward the top of the map mark the locations of genes superimposed on the physical map. Neighboring genes are offset slightly in the vertical axis for display purpose. Note one region of very high gene density from about 120 to 123 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. The orange hash marks along the X-axis represent the number of single nucleotide polymorphisms that distinguish the two parental strains (C57BL/6J and DBA/2J) from each other. We call this the SNP seismograph track (see Glossary for more details). Regions with low numbers of SNPs have closely matched sequences and are less likely to contain QTLs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. As before, the thin red line shows the additive effect size. By convention the positive values signify the D alleles are associated with higher expression of App in this region of Chr 7 than the B alleles. The maximum effect size is about +0.20 log2 expression units per D allele. The differences been the BB and DD genotypes (BB and DD because each strain has two alleles; one per chromosome) is therefore about 2^0.4 = 1.32 or a 32% increment in DD relative to BB at this locus.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. If you scroll just under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps are zoomable, a feature we will exploit to evaluate candidate genes in this QTL interval.</font><br> </td> </tr> </table> </div> </layer> <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/slide0021_image099.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image099.png deleted file mode 100755 index 891bc06c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image099.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image100.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image100.png deleted file mode 100755 index 8905caa6..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image100.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image101.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image101.png deleted file mode 100755 index 7f5a5295..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_image101.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_notes_pane.htm deleted file mode 100755 index b1988954..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0021_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm deleted file mode 100755 index 25d9a02e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022.htm +++ /dev/null @@ -1,134 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: 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; - - 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("slide0022.htm"); -}//--> -</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> - -g_origHeight = 566; 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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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.34 * g_height; myleft = 0.01 * g_width; myheight = 0.61 * g_height; mywidth = 0.97 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.34 * g_height; -ht = 0.61 * g_height; -wd = 0.97 * g_width; -document.write( -'<img border=0 src="slide0008_image076.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - 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 + ' >' ); -</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%'>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> - mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 0.34 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.08 * g_height; -ht = 0.22 * g_height; -wd = 0.34 * g_width; -document.write( -'<img border=0 src="slide0008_image077.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</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> - mytop = 0.17 * g_height; myleft = 0.75 * g_width; myheight = 0.14 * 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 * 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"> </span></i></span><span style='font-size:200%; color:#E9EB5D'><i>= better<br> </i></span></div> </layer><script> - mytop = 0.07 * 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 style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></span></div> </layer></div> </layer></div> </layer></div> </LAYER> - <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QTL gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </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/slide0022_image102.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image102.png deleted file mode 100755 index 5ab7794c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image102.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image103.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image103.png deleted file mode 100755 index c26d4792..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image103.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image104.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image104.png deleted file mode 100755 index af0745a5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image104.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image105.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image105.png deleted file mode 100755 index 6ec88720..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image105.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image106.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image106.png deleted file mode 100755 index 9c156ddc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_image106.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_notes_pane.htm deleted file mode 100755 index 4d30f6e3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0022_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The red line and the red axis to the far right provides an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>6. You can also download the results of the analysis in a text format</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023.htm deleted file mode 100755 index fabf25c5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023.htm +++ /dev/null @@ -1,115 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: Physical maps are zoomable"> <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("slide0023.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.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 maps are zoomable</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 = 0.08 * g_height; myleft = 0.03 * g_width; myheight = 0.41 * g_height; mywidth = 0.89 * 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 = 0.41 * g_height; -wd = 0.89 * g_width; -document.write( -'<img border=0 src="slide0009_image078.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.44 * g_height; myleft = 0.07 * g_width; myheight = 0.48 * g_height; mywidth = 0.42 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.07 * g_width; -yy = 0.44 * g_height; -ht = 0.48 * g_height; -wd = 0.42 * g_width; -document.write( -'<img border=0 src="slide0009_image079.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.94 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.97 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0 * g_width; -yy = 0.94 * g_height; -ht = 0.03 * g_height; -wd = 0.97 * g_width; -document.write( -'<img border=0 src="slide0009_image080.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>An even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image107.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image107.png deleted file mode 100755 index 0e63f836..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image107.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image108.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image108.png deleted file mode 100755 index 3c44c2ab..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_image108.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_notes_pane.htm deleted file mode 100755 index 010f3332..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0023_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <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>The map on the top has an X-axis scale based on frequency of recombinations events between markers (B to D transitions, see slide 19 for a color-coded example). These so-called genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast, the physical map shown below the genetic map has an X-axis scale based on DNA length measured in nucleotides or base-pairs. Notice the large difference between the two maps in the size of Chr 19 (large on the genetic scale but small on the physical scale).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Also notice the large difference in the width of the chromosome 7 QTL peak. In mice, recombinations occur with higher frequency toward the telomeric side (righ sidet) of each chromosome. As a result, genetic maps are stretched out more toward the telomere relative to a physical map. The QTL on distal Chr 7 is therefore actually more precisely mapped than might appear looking at the genetic map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>The physical scale is becoming more useful than the genetic scale primarily because many other data types can be easily superimposed on a physical map. You will see more examples in the next several slides.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024.htm deleted file mode 100755 index bf2b9b3c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024.htm +++ /dev/null @@ -1,167 +0,0 @@ -<html> <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="Aug-15-05: Evaluating Ctbp2 as a candidate QTL for App"> <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("slide0024.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - 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> - mytop = 0.94 * g_height; myleft = 0.03 * g_width; myheight = 0.04 * g_height; mywidth = 0.96 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.03 * g_width; -yy = 0.94 * g_height; -ht = 0.04 * g_height; -wd = 0.96 * g_width; -document.write( -'<img border=0 src="slide0010_image082.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0.03 * g_width; myheight = 0.4 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.03 * g_width; -yy = 0.07 * g_height; -ht = 0.4 * g_height; -wd = 0.48 * g_width; -document.write( -'<img border=0 src="slide0010_image083.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.52 * g_height; myleft = 0.55 * g_width; myheight = 0.37 * g_height; mywidth = 0.35 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;color:#E9EB5D'><i> the </i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2 </i></span><span style='font-size:233%;color:#E9EB5D'>cis QTL, </span></span></layer><script> - mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>but is detected </span></span></layer><script> - mytop = 0.18 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>only in the </span></span></layer><script> - mytop = 0.25 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>Rosen striatum </span></span></layer><script> - mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>data set.</span><span style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> - mytop = 0.16 * g_height; myleft = 0.56 * g_width; myheight = 0.12 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.45 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;color:#E9EB5D'><i> the App QTL </i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>in the INIA data set. </span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> - mytop = 0.39 * g_height; myleft = 0.03 * g_width; myheight = 0.53 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.03 * g_width; -yy = 0.39 * g_height; -ht = 0.53 * g_height; -wd = 0.48 * g_width; -document.write( -'<img border=0 src="slide0010_image084.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.35 * g_width; myheight = 0.72 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.35 * g_width; -yy = 0.1 * g_height; -ht = 0.72 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0010_image085.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.31 * g_width; myheight = 0.72 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.31 * g_width; -yy = 0.1 * g_height; -ht = 0.72 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0010_image086.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>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differences may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consistency of QTL peaks.</font><br> </td> </tr> </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/slide0024_image109.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image109.png deleted file mode 100755 index c0174c3f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image109.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image111.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image111.png deleted file mode 100755 index 9a3e3264..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_image111.png +++ /dev/null Binary files differdiff --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 deleted file mode 100755 index e6f07dec..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0024_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>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"> </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 diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025.htm deleted file mode 100755 index e9ce598f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025.htm +++ /dev/null @@ -1,104 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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: Evaluating Ctbp2 using other resources"> <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("slide0025.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.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%'>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> - mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.53 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.1 * g_height; -ht = 0.53 * g_height; -wd = 0.48 * g_width; -document.write( -'<img border=0 src="slide0011_image087.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.4 * g_height; myleft = 0.19 * g_width; myheight = 0.54 * g_height; mywidth = 0.78 * g_width; - 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; -wd = 0.78 * g_width; -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"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. You can get interesting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particular interest with respect to APP protein processing, Ctbp2 covaries positively with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </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 deleted file mode 100755 index 14e3fbe5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image112.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image113.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image113.png deleted file mode 100755 index ec9fff87..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_image113.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_notes_pane.htm deleted file mode 100755 index 19825b0d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0025_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QT gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026.htm deleted file mode 100755 index 2ef9b9ff..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026.htm +++ /dev/null @@ -1,139 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.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: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("slide0026.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0 * 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 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> - mytop = 0.15 * g_height; myleft = 0.05 * g_width; myheight = 0.31 * g_height; mywidth = 1.01 * 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 = 0.04 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.84 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.96%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Covered the basics of QTL analysis and mapping.<br> </span></span></layer></div> </layer><script> - mytop = 0.04 * 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'>2.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Reviewed difference between genetic and physical maps.<br> </span></span></layer></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 1.01 * 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 = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.55%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed interpreting features of QTL maps including the LRS function, </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>the additive effect function, the bootstrap bars, and the permutation </span></span></layer><script> - mytop = 0.09 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.84 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>thresholds.<br> </span></span></layer></div> </layer><script> - mytop = 0.22 * 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> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.04 * g_height; mywidth = 0.86 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.89%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Illustrated techniques to generate a list of positional candidates.<br> </span></span></layer></div> </layer><script> - mytop = 0.26 * 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'>5.</span></span><span style='font-family:"Gill Sans";font-size:167%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed some factors used to evaluate candidate genes.</span></span></layer></div> </layer></div> </layer><script> - mytop = 0.58 * g_height; myleft = 0.05 * g_width; myheight = 0.22 * g_height; mywidth = 1.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.89 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>What does a QTL signify? A good QTL is a claim that a particular </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.02 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>chromosomal region contains a causal source of variation in the phenotype. </span></span></layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>The importance of this hypothesis depends on the quality and relevance of the </span></span></layer><script> - mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.96 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>phenotype and the statistical strength of the QTL. As usual, test and be </span></span></layer><script> - mytop = 0.17 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.89 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:167%; color:#E9EB5D;mso-color-index:3'>skeptical.</span></span></layer></div> </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.ppt_files/slide0026_image114.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image114.png deleted file mode 100755 index 93d21c90..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image114.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image115.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image115.png deleted file mode 100755 index fdc27d23..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image115.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image116.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image116.png deleted file mode 100755 index d2cb5ee3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_image116.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_notes_pane.htm deleted file mode 100755 index d335b732..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0026_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <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>Even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027.htm deleted file mode 100755 index c553bae9..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027.htm +++ /dev/null @@ -1,115 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: Test Questions"> <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("slide0027.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.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%'>Test Questions</span><span style='font-family:Verdana;font-size:73%;mso-special-format: lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> - mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 1.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:233%;color:#E9EB5D'>1. Evaluate candidates for the Chr 3 </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> QTL.</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer><script> - mytop = 0.24 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>2. Do </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size: 233%;color:#E9EB5D'> and </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'> expression share any </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>other QTLs beside that on Chr 7?</span><span style='font-size:233%;color:#E9EB5D; mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> - mytop = 0.43 * g_height; myleft = 0.04 * g_width; myheight = 0.19 * g_height; mywidth = 1.02 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.02 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>3. Can you exploit literature mining tools to </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>find a strong relationship between </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> and </span></span></layer><script> - mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'>? </span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> - mytop = 0.69 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>4. Why might the cis QTL for </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'> expression </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>only be detected in the striatum data set?</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </LAYER> -<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/slide0027_image118.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image118.png deleted file mode 100755 index cf5f70f7..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image118.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image119.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image119.png deleted file mode 100755 index a5886d21..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image119.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image120.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image120.png deleted file mode 100755 index 7eb77319..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image120.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image121.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image121.png deleted file mode 100755 index 99f4d04d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image121.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image122.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image122.png deleted file mode 100755 index ac87ce02..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_image122.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_notes_pane.htm deleted file mode 100755 index 26d15c0e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0027_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differencess may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Verdana size=2> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consiistency of QTL peaks.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028.htm deleted file mode 100755 index 67711e7c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028.htm +++ /dev/null @@ -1,112 +0,0 @@ -<html> <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="Aug-15-05: Contact for comments and improvements:"> <style media=print> <!--.sld {left:0px !important; 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myleft = 0.06 * g_width; myheight = 0.24 * g_height; mywidth = 0.9 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.24 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br> </span></span></layer><script> - mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:82%'><br> </span></span></layer><script> - mytop = 0.16 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> - mytop = 0.27 * g_height; myleft = 0.09 * g_width; myheight = 0.07 * g_height; mywidth = 0.5 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'>kmanly@utmem.edu</span></div> </layer><script> - mytop = 0.83 * g_height; myleft = 0.04 * g_width; myheight = 0.15 * 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> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and R. Clark (July 15, </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>2005)</span><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D;mso-special-format:lastCR;display:none'><br> </span></span></layer></div> </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/html/webqtl_demo2.ppt_files/slide0028_image123.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image123.png deleted file mode 100755 index a6ca39ae..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image123.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image124.png b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image124.png deleted file mode 100755 index c17a41bc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_image124.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_notes_pane.htm deleted file mode 100755 index 3693ce68..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0028_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>Ctbp2 should also be considered a high priority biological candidate gene responsible for modulating App expression levels. The<span style="mso-spacerun: yes"> </span>C-terminal binding protein 2 is a transcriptional co-repressor also known as Ribeye.</font><font face=Times-Roman size=2> The gene produces two transcripts encoding distinct proteins. The short form is a transcriptional repressor that binds a Pro-X-Asp-Leu-Ser peptide motif common to adenoviral oncoprotein E1a and a related motif in BKLF. This short form also interacts<span style="mso-spacerun: yes"> </span>with several transcription factors including EVI1, ZFPM1, and<span style="mso-spacerun: yes"> </span>ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component of specialized synapses in photoreceptors. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br> </td> </tr> <tr> <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"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span style="mso-spacerun: yes"> </span>and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=2>3. You can get intersting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particualr interest with respect to APP protein processing, Ctbp2 covaries positiviely with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </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 diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0029.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0029.htm deleted file mode 100755 index 74ec8342..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0029.htm +++ /dev/null @@ -1,34 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate 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"> <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( "slide0029.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.ppt_files/slide0030.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0030.htm deleted file mode 100755 index 5562bbe5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0030.htm +++ /dev/null @@ -1,34 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! 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top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: Contact for comments and improvements:"> <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=Slide0014.gif border=0 usemap="#Slide0014.gif_map"></center> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0043.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0043.htm deleted file mode 100755 index e27e4083..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0043.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -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("slide0043.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0 * g_height; myleft = 0.01 * 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 = 0.9 * 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> - mytop = 0.08 * g_height; myleft = 0.05 * g_width; myheight = 0.91 * g_height; mywidth = 0.66 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.05 * g_width; -yy = 0.08 * g_height; -ht = 0.91 * g_height; -wd = 0.66 * g_width; -document.write( -'<img border=0 src="slide0012_image026.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>By clicking on the CORRELATION of the Atcay transcript to the App transcript, you can generate a Correlation plot between these two transcripts. In this App and Atcay scatterplot, each point is a strain mean value. For example, BXD33 and BXD8 have low App and Atcay expressions. The two parental strains and the F1 are also included in this plot.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0044.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0044.htm deleted file mode 100755 index ec5c2e3c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0044.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -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("slide0044.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.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> - mytop = 0.09 * g_height; myleft = 0.02 * g_width; myheight = 0.9 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.02 * g_width; -yy = 0.09 * g_height; -ht = 0.9 * g_height; -wd = 0.83 * g_width; -document.write( -'<img border=0 src="slide0013_image027.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>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 deleted file mode 100755 index 4e705866..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0045.htm +++ /dev/null @@ -1,118 +0,0 @@ -<html> <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: App transcript coexpression neighborhood"> <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("slide0045.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</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 + ' >' ); -</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> - mytop = 0.37 * g_height; myleft = 0.01 * g_width; myheight = 0.62 * g_height; mywidth = 0.97 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.37 * 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; -document.write( -'<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"> </span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use curved lines (aka ÒedgesÓ).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm deleted file mode 100755 index 93429543..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0046.htm +++ /dev/null @@ -1,104 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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> <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> - -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.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> - mytop = 0.28 * g_height; myleft = 0.04 * g_width; myheight = 0.7 * g_height; mywidth = 0.78 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.04 * g_width; -yy = 0.28 * g_height; -ht = 0.7 * g_height; -wd = 0.78 * g_width; -document.write( -'<img border=0 src="slide0015_image034.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</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; -yy = 0.08 * g_height; -ht = 0.19 * g_height; -wd = 0.33 * g_width; -document.write( -'<img border=0 src="slide0015_image035.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>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 deleted file mode 100755 index e7568e44..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0047.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html> <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> <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("slide0047.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.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.ppt_files/slide0048.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0048.htm deleted file mode 100755 index f36b1e25..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0048.htm +++ /dev/null @@ -1,151 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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> <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("slide0048.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 1:</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.08 * g_width; myheight = 0.47 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.84%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You have learned the basics about searching for traits<br> </span></span></layer></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.85 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-3.03%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know some methods to check data quality<br> </span></span></layer></div> </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"> </span>You know how to edit bad or suspicious data<br> </span></span></layer></div> </layer><script> - mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.85%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to review the basic statistics of a trait<br> </span></span></layer></div> </layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.74%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a scattergram between two </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>traits using the Traits Correlation tool<br> </span></span></layer></div> </layer><script> - mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; 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 + ' >' ); -</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:-2.56%;font-family:Arial'>6.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to add items to your SELECTIONS window<br> </span></span></layer></div> </layer><script> - mytop = 0.37 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.97 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.57%;font-family:Arial'>7.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a Network Graph of traits that </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>co-vary. </span></span></layer></div> </layer></div> </layer><script> - mytop = 0.67 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.05 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.05 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>What does genetic covariance mean? The genetic covariance can </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>be functional and mechanistic, but it can also be due to linkage </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; 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.ppt_files/slide0049.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0049.htm deleted file mode 100755 index 9d36600a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0049.htm +++ /dev/null @@ -1,155 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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: The GeneNetwork and WebQTL : PART 2 link to www.genenetwork.org"> <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("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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.03 * g_height; myleft = 0.02 * 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><script> - mytop = 0.02 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; 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> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:73%'>The GeneNetwork and WebQTL : PART 2<span style="mso-spacerun: yes"> </span><br> </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 0.89 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:73%'>link to www.genenetwork.org</span><span style='font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> - mytop = 0.24 * g_height; myleft = 0.05 * g_width; myheight = 0.68 * g_height; mywidth = 0.54 * 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 = 0.42 * g_height; mywidth = 0.52 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.21 * g_height; mywidth = 0.52 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.46 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 1. How to study </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>expression variation </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.47 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>and genetic correlation </span></span></layer><script> - mytop = 0.15 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 2–17)<br> </span></span></layer></div> </layer><script> - mytop = 0.25 * g_height; myleft = 0 * g_width; myheight = 0.16 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.46 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.43 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>upstream modulators </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0.05 * g_width; myheight = 0.06 * g_height; mywidth = 0.41 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:94%;color:#E9EB5D;mso-color-index: 3'>(slides 18–29)</span></span></layer></div> </layer></div> </layer></div> </layer><script> - mytop = 0.17 * g_height; myleft = 0.74 * g_width; myheight = 0.64 * g_height; mywidth = 0.23 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.74 * g_width; -yy = 0.17 * g_height; -ht = 0.64 * g_height; -wd = 0.23 * g_width; -document.write( -'<img border=0 src="slide0018_image037.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.75 * g_height; myleft = 0.74 * g_width; myheight = 0.14 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> </layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </layer></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 = 0.5 * g_height; myleft = 0.48 * g_width; myheight = 0.13 * g_height; mywidth = 0.25 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.48 * g_width; -yy = 0.5 * g_height; -ht = 0.13 * g_height; -wd = 0.25 * g_width; -document.write( -'<img border=0 src="slide0018_image038.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>Part 2: Discovering upstream modulators and quantitative trait loci (QTLs). A quantitative trait locus is a chromosomal region that harbors one or a few polymorphic gene loci that influence a trait. We are going to be looking for QTLs that modulate the steady state expression level of App in the adult mouse forebrain.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</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/slide0050.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0050.htm deleted file mode 100755 index 48469040..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0050.htm +++ /dev/null @@ -1,919 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); 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-</script> <div style='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;display:none'><br> </span></div> </layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.02 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='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 = 0.92 * g_height; myleft = 0.35 * g_width; myheight = 0.05 * g_height; mywidth = 0.29 * 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 = 0.02 * 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;display:none'><br> </span></div> </layer><script> - 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 + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-341 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-341 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Arial;font-size:300%; color:aqua'>B</span><span style='font-family:Arial;font-size:300%;color:#FFFF99'>X</span><span style='font-family:Arial;font-size:300%;color:#FF1911'>D</span></div> </layer></div> </layer><script> - mytop = 0.27 * g_height; myleft = 0.32 * g_width; myheight = 0.04 * g_height; mywidth = 0.31 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.32 * g_width; -yy = 0.27 * g_height; -ht = 0.04 * g_height; -wd = 0.31 * g_width; -document.write( -'<img border=0 src="slide0019_image083.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.66 * g_height; myleft = 0.6 * g_width; myheight = 0.03 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.6 * g_width; -yy = 0.66 * g_height; -ht = 0.03 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image084.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.64 * g_height; myleft = 0.15 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.15 * g_width; -yy = 0.64 * g_height; -ht = 0.05 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image085.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.57 * g_height; myleft = 0.75 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.75 * g_width; -yy = 0.57 * g_height; -ht = 0.05 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image086.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.28 * g_height; myleft = 0.48 * g_width; myheight = 0.08 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.48 * g_width; -yy = 0.28 * g_height; -ht = 0.08 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0019_image087.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.62 * g_height; myleft = 0.23 * g_width; myheight = 0.16 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.23 * g_width; -yy = 0.62 * g_height; -ht = 0.16 * g_height; -wd = 0.03 * g_width; -document.write( -'<img border=0 src="slide0019_image088.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.61 * g_height; myleft = 0.63 * g_width; myheight = 0.08 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.63 * g_width; -yy = 0.61 * g_height; -ht = 0.08 * g_height; -wd = 0.01 * g_width; -document.write( -'<img border=0 src="slide0019_image089.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>The next few slides provide a short introduction to mapping the loci that are responsible for variation in a trait such as App expression level. These modulatory regions of the genome are sometimes called quantitative trait loci or QTLs. You may want to do some independent reading on this topic if this is your first exposure to QTL analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The genetic reference population (GRP) of BXD recombinant inbred strains were originally generated about 25 years ago by Benjamin Taylor at The Jackson Laboratory. He crossed female C57BL/6J mice with male DBA/2J mice to generate the F1 and F2 progeny. At the bottom of this slide we have schematized one chromosome pair from three of the BXD RI strains.<span style="mso-spacerun: yes"> </span>The dashed vertical lines that lead to the final BXD RI lines involve 21 full sib matings (about 7 years of breeding). Some lines die out during inbreeding. For example, there is no longer any BXD3 strain.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. Over the last decade, our group (Lu Lu and Rob Williams) and Jeremy Peirce and Lee Silver at Princeton have enlarged Ben TaylorÕs set. There are now just over 80 BXD strains. They have all been genotyped using about 13,700 markers (SNPs and microsatellites). These markers are used to define the ÒblueÓ and ÒredÓ regions of the chromosomes as shown in the figure above.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. Chromosomes of RI GRPs usually have about 4 times as many recombinations as those of F2 animals. However, unlike an F2, both chromosomes of an RI are identical. Therefore, 50 RI strains contain as many recombinations as 100 F2 animals.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. BXD43 through BXD100 were generated using a special method that resulted in a further doubling of the average recombination density per chromosome. The entire set of 80 BXDs therefore contains as many recombinations as about 260 F2 animals.</font><br> </td> </tr> </table> </div> </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/slide0051.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0051.htm deleted file mode 100755 index 29b1f60e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0051.htm +++ /dev/null @@ -1,421 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); 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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:"-126 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:"-126 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:"-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="slide0020_image092.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="slide0020_image093.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="slide0020_image094.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.17 * g_height; myleft = 0.09 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> - mytop = 0.17 * g_height; myleft = 0.17 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> - mytop = 0.79 * g_height; myleft = 0.05 * g_width; myheight = 0.13 * g_height; mywidth = 1.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.12 * g_height; mywidth = 1.02 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-256 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-256 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.02 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E2EBF0'>D</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%; color:#E9EB5D'>and </span><span style='font-size:233%;color:#F6BF69'>B</span><span style='font-size:233%;color:#E9EB5D'> </span><span style='font-size:200%; color:#E9EB5D'>may be SNP-like variants in the promoter </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 1.02 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'>itself (cis QTL) or in </span><span style='font-size:200%;color:#EAEC5E'>upstream genes (trans QTLs)</span><span style='font-size:300%;color:#E9EB5D'>.</span></span></layer></div> </layer></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0.04 * g_width; myheight = 0.16 * g_height; mywidth = 0.22 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>UPSTREAM<br> </span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.22 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D'>modulators<br> </span></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.05 * g_height; mywidth = 0.2 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-233 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-size:200%;color:#E9EB5D; mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0.44 * g_width; myheight = 0.17 * g_height; mywidth = 0.16 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:300%;color:#E2EBF0'>High<br> </span></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:16;mso-text-indent-alt: 16'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.63 * g_height; myleft = 0.08 * g_width; myheight = 0.17 * g_height; mywidth = 0.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0'>D<br> </span></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#E2EBF0;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.63 * g_height; myleft = 0.15 * g_width; myheight = 0.17 * g_height; mywidth = 0.05 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.16 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.04 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69'>B<br> </span></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-350 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:300%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.71 * g_height; myleft = 0.07 * g_width; myheight = 0.12 * g_height; mywidth = 0.16 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.1 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.14 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D'><i>cis QTL</i></span><span style='font-size:200%;color:#E9EB5D;display:none'><br> </span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.57 * g_height; myleft = -0.01 * g_width; myheight = 0.07 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = -0.01 * g_width; -yy = 0.57 * g_height; -ht = 0.07 * g_height; -wd = 1.01 * g_width; -document.write( -'<img border=0 src="slide0020_image095.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.44 * g_height; myleft = 0.47 * g_width; myheight = 0.12 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69'>Low<br> </span></div> </layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.07 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-272 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:233%;color:#F6BF69;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> - mytop = 0.58 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.04 * g_height; mywidth = 1.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17;mso-line-spacing:"-200 0 0";mso-margin-left-alt:17; mso-text-indent-alt:17'><span style='font-family:Gadget;font-size:167%; color:white'>>>>>PROMOTER--ATG-Exon1-Intron1-Exon2-Intron2 - etc-3'UTR >>>>></span></div> </layer></div> </layer><script> - mytop = 0.37 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.08 * g_width; -yy = 0.37 * g_height; -ht = 0.2 * g_height; -wd = 0.13 * g_width; -document.write( -'<img border=0 src="slide0020_image096.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.4 * g_height; myleft = 0.1 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> - mytop = 0.4 * g_height; myleft = 0.18 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> - mytop = 0.33 * g_height; myleft = 0.08 * g_width; myheight = 0.2 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.08 * g_width; -yy = 0.33 * g_height; -ht = 0.2 * g_height; -wd = 0.13 * g_width; -document.write( -'<img border=0 src="slide0020_image097.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.36 * g_height; myleft = 0.18 * g_width; myheight = 0.11 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:center;mso-line-spacing:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:"\30D2\30E9\30AE\30CE\89D2\30B4 Pro W3"; font-size:233%;color:white'><b></b></span><span style='font-family:Palatino; font-size:233%;color:white;display:none'><b><br> </b></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); 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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:"-269 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:"-269 0 0";mso-margin-left-alt: 17;mso-text-indent-alt:17'><span style='font-family:Palatino;font-size:233%; color:white;mso-special-format:lastCR;display:none'><b><br> </b></span></div> </layer></div> </layer><script> - mytop = 0.27 * 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="slide0020_image098.png" 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 = 0.2 * 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> - 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:"-233 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-size:200%;color:#E9EB5D;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer></div> </layer></div> </LAYER> - <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"> </span>The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be indirect. Effects can:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>a.<span style="mso-spacerun: yes"> </span>cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>b.<span style="mso-spacerun: yes"> </span>cross time (the modulator is only expressed for one day during development but has permanent effects in adults)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3><span style="mso-spacerun: yes"> </span>c.<span style="mso-spacerun: yes"> </span>may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm deleted file mode 100755 index 7a2e03db..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0052.htm +++ /dev/null @@ -1,115 +0,0 @@ -<html> <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: Discovering upstream modulatory loci"> <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("slide0052.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.38 * g_height; myleft = 0.05 * g_width; myheight = 0.45 * g_height; mywidth = 0.84 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.05 * g_width; -yy = 0.38 * g_height; -ht = 0.45 * g_height; -wd = 0.84 * g_width; -document.write( -'<img border=0 src="slide0021_image099.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.08 * g_height; mywidth = 0.93 * 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 = 0.91 * 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> - mytop = 0.2 * g_height; myleft = 0.18 * g_width; myheight = 0.25 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.18 * g_width; -yy = 0.2 * g_height; -ht = 0.25 * g_height; -wd = 0.19 * g_width; -document.write( -'<img border=0 src="slide0021_image100.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.32 * g_height; myleft = 0.78 * g_width; myheight = 0.25 * g_height; mywidth = 0.19 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.78 * g_width; -yy = 0.32 * g_height; -ht = 0.25 * g_height; -wd = 0.19 * g_width; -document.write( -'<img border=0 src="slide0021_image101.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>Please bring the Trait Data and Analysis window to the front and look for the Interval Mapping button. Confirm that you are back to the trait amyloid beta precursor protein.<span style="mso-spacerun: yes"> </span>If so, then just click the button.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notice that the default for:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Chrs (chromosomes) is ALL</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Select Mapping Scale is set to GENETIC</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Permutation test YES<span style="mso-spacerun: yes"> </span>(2000 is the default number)</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Options: Bootstrap test YES (2000 is the default number)</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</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 deleted file mode 100755 index d729b467..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0053.htm +++ /dev/null @@ -1,155 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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: WebQTL searches for upstream controllers"> <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("slide0053.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.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 = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0;mso-line-spacing:"-358 0 -1";mso-margin-left-alt:233; mso-text-indent-alt:0'><span style='font-family:Verdana;font-size:64%'><i>WebQTL searches for upstream controllers</i></span><span style='font-family:Verdana; font-size:73%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> - mytop = 0.71 * g_height; myleft = 0.34 * g_width; myheight = 0.19 * g_height; mywidth = 0.45 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.18 * g_height; mywidth = 0.44 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.44 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>App maps on Chr 16 (blue </i></span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.44 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>arrow points to the orange </i></span></span></layer><script> - mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.38 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>triangle) but the best </i></span></span></layer><script> - mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.38 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D'><i>locus is on Chr 7.</i></span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.53 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.08 * g_height; -ht = 0.53 * g_height; -wd = 0.98 * g_width; -document.write( -'<img border=0 src="slide0022_image102.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.46 * g_height; myleft = 0.15 * g_width; myheight = 0.53 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.15 * g_width; -yy = 0.46 * g_height; -ht = 0.53 * g_height; -wd = 0.15 * g_width; -document.write( -'<img border=0 src="slide0022_image103.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.46 * g_height; myleft = 0.8 * g_width; myheight = 0.53 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.8 * g_width; -yy = 0.46 * g_height; -ht = 0.53 * g_height; -wd = 0.1 * g_width; -document.write( -'<img border=0 src="slide0022_image104.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.41 * g_height; myleft = 0.76 * g_width; myheight = 0.22 * g_height; mywidth = 0.11 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.76 * g_width; -yy = 0.41 * g_height; -ht = 0.22 * g_height; -wd = 0.11 * g_width; -document.write( -'<img border=0 src="slide0022_image105.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.41 * g_height; myleft = 0.29 * g_width; myheight = 0.24 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.29 * g_width; -yy = 0.41 * g_height; -ht = 0.24 * g_height; -wd = 0.12 * g_width; -document.write( -'<img border=0 src="slide0022_image106.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>This is a major output type: a so-called full-genome interval map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The X-axis represents all 19 autosomes and the X chromosome as if they were laid end to end with short gaps between the telomere of one chromosome and the centromere of the next chromosome (mouse chromosomes only have a single long arm and the centromere represents the origin of each chromosome for numerical purpose: 0 centimorgans at almost 0 megabases). The blue labels along the bottom of the figure list a subset of the 3795 markers that were used in mapping.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The thick blue wavy line running across chromosomes summarizes the strength of association between variation in the phenotype (App expression differences) and the two genotypes of all markers and the intervals between markers (hence, interval mapping).<span style="mso-spacerun: yes"> </span>The height of the wave (blue Y-axis to the left) provides the likelihood ratio statistic (LRS). Divide by 4.61 to convert these values to LOD scores.<span style="mso-spacerun: yes"> </span>Or you can read them as a chi-square-like statistic.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The red line and the red axis to the far right provides an estimate of the effect that a QTL has on expression of App (this estimate of the so-called additive effect tends to be too high). If the red line is below the X-axis then this means that the allele inherited from C57BL/6J (B6 or B) at a particular marker is associated with higher values. If the red line is above the X-axis then the DBA/2J allele (D2 or D) is associated with higher trait values. Multiply the additive effect size by 2 to estimate the difference between the set of strains that have the B/B genotype and those that have the D/D genotype at a specific marker. For example, on distal Chr 7 the red line peaks at a value of about 0.2. That means that this region of chromosome 2 is responsible for a 0.4 unit expression difference between B/B strains and the D/D strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The yellow histogram bars: These summarize the results of a whole-genome bootstrap of the trait that is performed 1000 times. What is a bootstrap? A bootstrap provides a method to evaluate whether results are robust. If we drop out one strain, do we still get the same results? When mapping quantitative traits, each strain normally gets one equally weighted vote. But using the bootstrap procedure, we give each strain a random weighting factor of between 0 and 1.<span style="mso-spacerun: yes"> </span>We then remap the trait and find THE SINGLE BEST LRS VALUE per bootstrap. We do this 1000 times. In this example, most bootstrap results cluster on Chr 3 and Chr 7 under the LRS peaks. That is somewhat reassuring. But notice that a substantial number of bootstrap are scattered around on other chromosomes. About 30% of the bootstrap resamples have a peak on Chr 7. That is pretty good, but does makes us realize that the sample we are working with is still quite small and fragile.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The horizontal dashed lines at 10.5 and 17.3 are the likelihood ratio statistic (LRS) values associated with the suggestive and significant genome-wide probabilities that were established by permutations of phenotypes across genotypes. We shuffle randomly 2000 times and obtain a distribution of peak LRS scores to generate a null distribution. Five percent of the time, one of these permuted data sets will have a peak LRS higher than 17.3. We call that level the 0.05 significance threshold for a whole genome scan. The p = 0.67 point is the the suggestive level, and corresponds to the green dashed line.<span style="mso-spacerun: yes"> </span>These thresholds are conservative for transcripts that have expression variation that is highly heritable. The putative or suggestive QTL on Chr 3 is probably more than just suggestive.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>One other point: the mapping procedure we use is computationally very fast, but it is relatively simple. We are not looking for gene-gene interactions and we are not fitting multiple QTLs in combinations. Consider this QTL analysis a first pass that will highlight hot spots and warm spots that are worth following up on using more sophisticated models.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>CLICKABLE REGIONS:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>1. If you click on the Chromosome number then you will generate a new map just for that chromosome.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. If you click on the body of the map, say on the blue line, then you will generate a view on a 10 Mb window of that part of the genome from the UCSC Genome Browser web site.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. If you click on a marker symbol, then you will generate a new Trait data and Analysis window with the genotypes loaded into the window just like any other trait. More on this in Section 3.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. You can drag these maps off of the browser window and onto your desktop. They will be saved as PNG or PDF files. You can import them into Photoshop or other programs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. There is also an option at the bottom of the page to download a 2X higher resolution image of this plot for papers and presentations.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>6. You can also download the results of the analysis in a text format</font><br> </td> </tr> </table> </div> </layer> <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/slide0054.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0054.htm deleted file mode 100755 index 64dbe68f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0054.htm +++ /dev/null @@ -1,113 +0,0 @@ -<html> <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: Genetic versus Physical maps for App expression"> <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("slide0054.htm"); -}//--> -</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> - -g_origHeight = 566; -g_origWidth = 755; 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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 = 0.01 * g_width; myheight = 0.08 * g_height; mywidth = 1.16 * 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 = 1.15 * 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>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> - mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.39 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.08 * g_height; -ht = 0.39 * g_height; -wd = 0.98 * g_width; -document.write( -'<img border=0 src="slide0023_image107.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.35 * g_height; myleft = 0.01 * g_width; myheight = 0.54 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.35 * g_height; -ht = 0.54 * g_height; -wd = 0.98 * g_width; -document.write( -'<img border=0 src="slide0023_image108.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.91 * g_height; myleft = 0.05 * 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:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow: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 = 0.95 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>The difference between genetic and physical scale is analogous to measuring the </i></span></span></layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:117%;color:#E9EB5D'><i>separation between New York and Boston in either travel hours or kilometers</i></span><span style='font-size:150%;color:#E9EB5D'><i>.</i></span><span style='font-size: 167%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </LAYER> - <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>The map on the top has an X-axis scale based on frequency of recombinations events between markers (B to D transitions, see slide 19 for a color-coded example). These so-called genetic maps are scaled in centimorgan (recombinations per 100 gametes). In contrast, the physical map shown below the genetic map has an X-axis scale based on DNA length measured in nucleotides or base-pairs. Notice the large difference between the two maps in the size of Chr 19 (large on the genetic scale but small on the physical scale).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Also notice the large difference in the width of the chromosome 7 QTL peak. In mice, recombinations occur with higher frequency toward the telomeric side (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><!-- -//--> -</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/slide0055.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0055.htm deleted file mode 100755 index cae5b4b9..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0055.htm +++ /dev/null @@ -1,110 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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: 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> -<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("slide0055.htm"); -}//--> -</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> - -g_origHeight = 566; -g_origWidth = 755; 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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 = 0.01 * 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> - mytop = 0.93 * g_height; 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The QTL peak is roughly between 120 and 132 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The small irregular colored blocks and marks toward the top of the map mark the locations of genes superimposed on the physical map. Neighboring genes are offset slightly in the vertical axis for display purpose. Note one region of very high gene density from about 120 to 123 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. The orange hash marks along the X-axis represent the number of single nucleotide polymorphisms that distinguish the two parental strains (C57BL/6J and DBA/2J) from each other. We call this the SNP seismograph track (see Glossary for more details). Regions with low numbers of SNP have closely matched sequences and are less likely to contain QTLs.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4. As before, the thin red line shows the additive effect size. By convention the positive values signify the D alleles are associated with higher expression of App in this region of Chr 7 than the B alleles. The maximum effect size is about +0.20 log2 expression units per D allele. The differences been the BB and DD genotypes (BB and DD because each strain has two alleles; one per chromosome) is therefore about 2^0.4 = 1.32; or a 32% increment in DD relative to BB at this locus.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5. If you scroll just under the Physical Map you will see text that reads ÒDISPLAY from XXX Mb TO YYY MbÉ..Ó<span style="mso-spacerun: yes"> </span>These physical maps are zoomable, a feature we will exploit to evaluate candidate genes in this QTL interval.</font><br> </td> </tr> </table> </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 deleted file mode 100755 index eba3fc05..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0056.htm +++ /dev/null @@ -1,134 +0,0 @@ -<html> <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; - - 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("slide0056.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.34 * g_height; myleft = 0.01 * g_width; myheight = 0.61 * g_height; mywidth = 0.97 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.34 * g_height; -ht = 0.61 * g_height; -wd = 0.97 * g_width; -document.write( -'<img border=0 src="slide0025_image112.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - 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 + ' >' ); -</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%'>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> - mytop = 0.08 * g_height; myleft = 0.01 * g_width; myheight = 0.22 * g_height; mywidth = 0.34 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.08 * g_height; -ht = 0.22 * g_height; -wd = 0.34 * g_width; -document.write( -'<img border=0 src="slide0025_image113.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</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> - mytop = 0.17 * g_height; myleft = 0.75 * g_width; myheight = 0.14 * 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 * 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"> </span></i></span><span style='font-size:200%; color:#E9EB5D'><i>= better<br> </i></span></div> </layer><script> - mytop = 0.07 * 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 style='text-align:center'><span style='font-size:200%;color:#E9EB5D'><i>candidates</i></span></div> </layer></div> </layer></div> </layer></div> </LAYER> - <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4><b>Evaluating candidate genes (CHECKED BOXES) responsible for variability in APP expression:</b></font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>A large number of genes are usually in the QTL interval and are therefore POSITIONAL CANDIDATES, but they will differ greatly in their biological and bioinformatic plausibility. Assume that the QTL has been located between 119 and 131 Mb (12 Mb). There will typically be 12 to 15 genes per Mb, so we might need to evaluate several hundred positional candidates. In this particular case there are about 100 known genes in this interval. Eight of these are highlighted in the table above with check marks in the boxes to the left.<span style="mso-spacerun: yes"> </span>We need to highlight and objectively score the biologically relevant subset of all 100 positional candidate genes. We could look through gene ontologies and expression levels to help us shorten the list. An alternate way available using WebQTL is to generate a list of those genes in this interval that have transcripts that co-vary in expression with App expression. That is what the table shows.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. To replicate this table go back to the Trait Data and Analysis Form. Choose to sort correlations by POSITION and select RETURN = 500. Then scroll down the list to Chr 7 and review the subset of positional candidates that share expression with App. You should see a list similar to that shown above. Gtf3c1 is a good biological candidate and has a high covariation in expression with App.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>2. Caveat:<span style="mso-spacerun: yes"> </span>Of course, the gene or genes that control App expression may not be in this list. A protein coding difference might be the ultimate cause of variation in App transcript level and the expression covariation might be close to zero. Our list may also simply be missing the right transcript since the microarray is not truly comprehensive. Furthermore, even if the list contains the QT gene, an expression difference may only have been expressed early in development or even in another tissue such as liver. While it is important to recognize these caveats, it is equally important to devise a rational way to rank candidates given existing data. Coexpression is one of several criteria used to evaluate positional candidates. We will see others in the next slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>3. We can also assess the likelihood that candidates contain functional polymorphism in promoters and enhancers that affect their expression simply by mapping the transcripts of all candidate genes to see if they Òmap backÓ to the location of gene itself. A transcript that maps to its own location is referred to as a cis QTL. We essentially ask: Which of the the transcripts listed in the Correlation Table above (from Gtf3c1 to Zranb1) has variation in expression that maps to Chr 7 at about 120 Mb?<span style="mso-spacerun: yes"> </span>The logic of this search is that if a gene controls the level of its own expression it is also much more likely to generate other downstream effects. The Gtf3c1 transcript is a weak cis QTL with a local LRS maximum of about 7.0 (D alleles are high). That is just about sufficient to declare it to be a cis QTL. [No whole genome correction is required and a point-wise p-value of 0.05 is the appropriate test. A p-value of 0.05 is roughly equivalent to an LRS of 6.0 (LOD = 1.3).]</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </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/slide0057.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0057.htm deleted file mode 100755 index dcc5ede7..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0057.htm +++ /dev/null @@ -1,115 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Jul-18-05: Physical maps are zoomable"> <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("slide0057.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.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 maps are zoomable</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 = 0.08 * g_height; myleft = 0.03 * g_width; myheight = 0.41 * g_height; mywidth = 0.89 * 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 = 0.41 * g_height; -wd = 0.89 * g_width; -document.write( -'<img border=0 src="slide0026_image114.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.44 * g_height; myleft = 0.07 * g_width; myheight = 0.48 * g_height; mywidth = 0.42 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.07 * g_width; -yy = 0.44 * g_height; -ht = 0.48 * g_height; -wd = 0.42 * g_width; -document.write( -'<img border=0 src="slide0026_image115.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.94 * g_height; myleft = 0 * g_width; myheight = 0.03 * g_height; mywidth = 0.97 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0 * g_width; -yy = 0.94 * g_height; -ht = 0.03 * g_height; -wd = 0.97 * g_width; -document.write( -'<img border=0 src="slide0026_image116.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>Even higher blow-up of part of the Chr 7 physical map of variation in App expression in brain.<span style="mso-spacerun: yes"> </span>The QTL region actually extends from about 119 to 129.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>1. As mentioned in the previous slide another important approach to ranking candidates is based on the number of sequence variants that distinguish the parental strains. If we were sure that the sequences of the gene, its promoter, and its enhancers were identical between the strains then we could discount--but not eliminate--that gene as a candidate. The Gtf3c1 candidate almost falls into this category: of 663 known SNPs in and around this gene, only four differ between C57BL/6J and DBA/2J. Gtf3c1 is essentially identical-by-descent in these strains and is a less likely candidate. In contrast, if the two alleles of the gene have dozens of functional variants in exons, promoters, enhancers, and splice sites, then it becomes a higher priority candidate.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face="Times New Roman" size=4>Of course it only takes a single critical sequence variant to generate downstream effects. The argument above is really about the prior probabilities. Where would you place your bets given the information at hand?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2.<span style="mso-spacerun: yes"> </span>If you scroll down the INTERVAL ANALYST you will find that Ctbp2 is a particularly interesting candidate that contains lots of SNPs (n = 75 and a SNP density of 0.55 SNP/Kb). Ctbp2 is also closer to our QTL peak than was Gtf3c1. Not only does Ctbp2 contain lots of SNPs but it is also is associated with a powerful cis QTL with an LRS of 24.2 (divide by 4.61 to get the equivalent LOD score of 5.25).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3.<span style="mso-spacerun: yes"> </span>At this high magnification, individual genes are distinct. They are color coded by their density of SNPs. Bright orange represents those genes that have a high SNP density (C57BL/6J versus DBA/2J), black represents genes with low SNP density. Roll the cursor over a gene block and its name will pop up, along with information on exon number.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>4.<span style="mso-spacerun: yes"> </span>Beneath the physical map you will find an INTERVAL ANALYST table that lists information on known genes in the region on which you have zoomed the Physical Map.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>5.<span style="mso-spacerun: yes"> </span>As always: error-checking is important. Some genes may be missing from the Interval Analyst (recent additions or errors of omission). In this case the Zranb1 gene that is located just proximal to Ctbp2 is not listed in the INTERVAL ANALYST. Double-check the interval using the Genome Browser links (blue and beige horizontal bars) at the top of the PHYSICAL MAP.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm deleted file mode 100755 index 47e08c87..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0058.htm +++ /dev/null @@ -1,167 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Jul-18-05: Evaluating Ctbp2 as a candidate QTL for App"> <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("slide0058.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - 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> - mytop = 0.94 * g_height; myleft = 0.03 * g_width; myheight = 0.04 * g_height; mywidth = 0.96 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.03 * g_width; -yy = 0.94 * g_height; -ht = 0.04 * g_height; -wd = 0.96 * g_width; -document.write( -'<img border=0 src="slide0027_image118.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0.03 * g_width; myheight = 0.4 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.03 * g_width; -yy = 0.07 * g_height; -ht = 0.4 * g_height; -wd = 0.48 * g_width; -document.write( -'<img border=0 src="slide0027_image119.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.52 * g_height; myleft = 0.55 * g_width; myheight = 0.37 * g_height; mywidth = 0.35 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;color:#E9EB5D'><i> the </i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.34 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2 </i></span><span style='font-size:233%;color:#E9EB5D'>cis QTL, </span></span></layer><script> - mytop = 0.12 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>but is detected </span></span></layer><script> - mytop = 0.18 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>only in the </span></span></layer><script> - mytop = 0.25 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.35 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>Rosen striatum </span></span></layer><script> - mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>data set.</span><span style='font-size:233%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> - mytop = 0.16 * g_height; myleft = 0.56 * g_width; myheight = 0.12 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.45 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>This is</span><span style='font-size:233%;color:#E9EB5D'><i> the App QTL </i></span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>in the INIA data set. </span><span style='font-size:233%;color:#E9EB5D;mso-special-format: lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> - mytop = 0.39 * g_height; myleft = 0.03 * g_width; myheight = 0.53 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.03 * g_width; -yy = 0.39 * g_height; -ht = 0.53 * g_height; -wd = 0.48 * g_width; -document.write( -'<img border=0 src="slide0027_image120.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.35 * g_width; myheight = 0.72 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.35 * g_width; -yy = 0.1 * g_height; -ht = 0.72 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0027_image121.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.31 * g_width; myheight = 0.72 * g_height; mywidth = 0 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.31 * g_width; -yy = 0.1 * g_height; -ht = 0.72 * g_height; -wd = 0 * g_width; -document.write( -'<img border=0 src="slide0027_image122.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>This slide illustrates one reason why Ctbp2 should be considered a high priority positional candidate gene that may modulate the expression level of App.<span style="mso-spacerun: yes"> </span>Ctbp2 is a strong cis QTL in some brain regions (here the data are taken from the striatum).<span style="mso-spacerun: yes"> </span>If Ctbp2 contains variants that modulate its own expression then these expression differencess may produce many downstream effects. Of course, we now want to know much more about the known biology of Ctbp2. What kind of gene is it? To begin to answer that question we can use a number of resources listed in the LINKS page.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Verdana size=3> The App QTL is bimodal. Perhaps there are actually two causal factors in this region--one close to 123 Mb and the other close to 127 Mb.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>2. The precision of QTL mapping depends on several factors, including the effect size and interactions among QTLs modulating a trait, the number of genetic individuals that are studied, and the distribution of recombinations in the study population.<span style="mso-spacerun: yes"> </span>In the case above, the QTL(s) are likely to be confined to the interval from 120 to 132 Mb. The bootstrap test (yellow bars shown in some of the previous slides) can be usual for estimating the consiistency of QTL peaks.</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/slide0059.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0059.htm deleted file mode 100755 index 5ba9ff5c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0059.htm +++ /dev/null @@ -1,104 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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 Ctbp2 using other resources"> <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("slide0059.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.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%'>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> - mytop = 0.1 * g_height; myleft = 0.01 * g_width; myheight = 0.53 * g_height; mywidth = 0.48 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.1 * g_height; -ht = 0.53 * g_height; -wd = 0.48 * g_width; -document.write( -'<img border=0 src="slide0028_image123.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.4 * g_height; myleft = 0.19 * g_width; myheight = 0.54 * g_height; mywidth = 0.78 * g_width; - 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; -wd = 0.78 * g_width; -document.write( -'<img border=0 src="slide0028_image124.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<span style="mso-spacerun: yes"> </span>C-terminal binding protein 2 is a transcriptional co-repressor also known as Ribeye.</font><font face=Times-Roman size=3> The gene produces two transcripts encoding distinct proteins. The short form is a transcriptional repressor that binds a Pro-X-Asp-Leu-Ser peptide motif common to adenoviral oncoprotein E1a and a related motif in BKLF. This short form also interacts<span style="mso-spacerun: yes"> </span>with several transcription factors including EVI1, ZFPM1, and<span style="mso-spacerun: yes"> </span>ZFHX1A (aka TCF8, deltaEF1). The longer isoform is a major component of specialized synapses in photoreceptors. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </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"> </span>http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene<span style="mso-spacerun: yes"> </span>and enter each gene symbol.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Verdana size=3>3. You can get intersting hints regarding Ctbp2 expression partners by examining the genetic correlations between Ctbp2 probe set 1422887_a_at and all other transcripts on the M430 Affymetrix array. Use the Striatum data set because we already know from previous work (the previous slide) that this gene is a cis QTL.<span style="mso-spacerun: yes"> </span>You should be able to show that Ctbp2 and Notch3 have antagonistic expression patterns in striatum. The negative genetic correlation with E2f4 is even stronger. The transcript also has a high positive genetic correlation with Rdh14. Of particualr interest with respect to APP protein processing, Ctbp2 covaries positiviely with Bace2 (the transcript of the beta site APP-cleaving enzyme 2).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </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/slide0060.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm deleted file mode 100755 index 2f1c5b7b..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0060.htm +++ /dev/null @@ -1,139 +0,0 @@ -<html> <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> <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("slide0060.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0 * 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 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> - mytop = 0.09 * g_height; myleft = 0.08 * g_width; myheight = 0.37 * g_height; mywidth = 1.02 * 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 = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.84 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.96%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Covered the basics of QTL analysis and mapping.<br> </span></span></layer></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.95 * 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 = 0.92 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.71%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Reviewed difference between genetic and physical maps.<br> </span></span></layer></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.15 * g_height; mywidth = 1.01 * 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 = 0.95 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.62%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed interpreting features of QTL maps including the </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>LRS function, the additive effect function, the bootstrap bars, </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.84 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>and the permutation thresholds.<br> </span></span></layer></div> </layer><script> - mytop = 0.26 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.02 * 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 = 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'><span style='mso-special-format:numbullet; position:absolute;left:-2.51%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Illustrated technics to generate a list of positional candidates.<br> </span></span></layer></div> </layer><script> - mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.97 * 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 = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.65%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>Discussed some factors used to evaluate candidate genes.</span></span></layer></div> </layer></div> </layer><script> - mytop = 0.58 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.06 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>What does a QTL signify? A good QTL is a claim that a particular </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>chromosomal region contains a causal source of variation in the </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>phenotype. The importance of this hypothesis depends on the </span></span></layer><script> - mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.92 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>quality and relevance of the phenotype and the statistical </span></span></layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.89 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>strength of the QTL. As usual, test and be skeptical.</span></span></layer></div> </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.ppt_files/slide0061.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0061.htm deleted file mode 100755 index a2816092..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0061.htm +++ /dev/null @@ -1,112 +0,0 @@ -<html> <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: Test Questions"> <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("slide0061.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.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%'>Test Questions</span><span style='font-family:Verdana;font-size:73%;mso-special-format: lastCR;display:none'><i><br> </i></span></div> </layer></div> </layer><script> - mytop = 0.11 * g_height; myleft = 0.04 * g_width; myheight = 0.06 * g_height; mywidth = 1.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-size:233%;color:#E9EB5D'>1. Evaluate candidates for the Chr 3 </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size:233%;color:#E9EB5D'> QTL.</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </layer><script> - mytop = 0.24 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>2. Do </span><span style='font-size:233%;color:#E9EB5D'><i>App</i></span><span style='font-size: 233%;color:#E9EB5D'> and </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'> expression share any </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>other QTLs beside that on Chr 7?</span><span style='font-size:233%;color:#E9EB5D; mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer><script> - mytop = 0.45 * 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> - mytop = 0.66 * g_height; myleft = 0.04 * g_width; myheight = 0.12 * g_height; mywidth = 1.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 1.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>4. Why might the cis QTL for </span><span style='font-size:233%;color:#E9EB5D'><i>Ctbp2</i></span><span style='font-size:233%;color:#E9EB5D'> expression </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:233%;color:#E9EB5D'>only be detected in the striatum data set?</span><span style='font-size:233%; color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></span></layer></div> </layer></div> </LAYER> -<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/slide0062.htm b/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0062.htm deleted file mode 100755 index 6b671799..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2.ppt_files/slide0062.htm +++ /dev/null @@ -1,109 +0,0 @@ -<html> <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: 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() { - 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("slide0062.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</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; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.24 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br> </span></span></layer><script> - mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:82%'><br> </span></span></layer><script> - mytop = 0.16 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> - mytop = 0.27 * g_height; myleft = 0.09 * g_width; myheight = 0.07 * g_height; mywidth = 0.5 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'>kmanly@utmem.edu</span></div> </layer><script> - mytop = 0.83 * g_height; myleft = 0.04 * g_width; myheight = 0.1 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.98 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>The </span><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'><i>App</i></span><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D'> findings reviewed in this presentation are part of an </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>ongoing study of R. 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100755 index 2d4aa484..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline.gif +++ /dev/null Binary files differdiff --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 deleted file mode 100755 index 4c804d69..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapse.gif +++ /dev/null Binary files differdiff --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 deleted file mode 100755 index 5da9503b..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_collapsed.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Robots content=NoIndex> <style> <!--a {text-decoration: none;}--> </style> </head> <body bgcolor=black text=white link=white vlink=white alink=white onload=" parent.base.highlite();" onresize="self.location.reload();"> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>GeneNetwork and WebQTL:</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>Slide 2</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Slide 3</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF><font face="Gill Sans">Search results</font></a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>"First page of data:"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>"Data sources:"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>"Expression estimates for App on..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>"Critiquing the App data the..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>"App expression after windsorizing"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>"Discovering shared expression patterns"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>"Transcript neighborhoods"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"App and Atcay transcript scatterplot"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>"App transcript and eight of..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>App transcript coexpression neighborhood</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID15 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p15" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('15')" id=AREF>"Correlations of App with classical..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID16 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p16" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('16')" id=AREF>"Network Graph of App with..."</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID17 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p17" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('17')" id=AREF>"Summary of Part 1:"</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID18 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p18" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('18')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expand.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expand.gif deleted file mode 100755 index c8c72b13..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expand.gif +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expanded.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expanded.htm deleted file mode 100755 index a45e9c0c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_expanded.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 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> <style> <!--a {text-decoration: none;}--> </style> </head> <body bgcolor=black text=white link=white vlink=white alink=white onload=" parent.base.highlite();" onresize="self.location.reload();"> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID1 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p1" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('1')" id=AREF>GeneNetwork and WebQTL:</a></b></font></td> </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 2–16)</font></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Part 2. Discovering upstream modulators (slides 17–30)</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID2 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p2" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('2')" id=AREF>Slide 2</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID3 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p3" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('3')" id=AREF>Slide 3</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID4 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p4" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('4')" id=AREF><font face="Gill Sans">Search results</font></a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID5 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p5" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('5')" id=AREF>"First page of data:"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>First page of data: The Trait Data and Analysis Form</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID6 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p6" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('6')" id=AREF>"Data sources:"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Data sources: Metadata for each resource</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID7 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p7" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('7')" id=AREF>"Expression estimates for App on..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Expression estimates for App on the Trait Data form</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID8 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p8" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('8')" id=AREF>"Critiquing the App data the..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Critiquing the App data the Trait Data</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID9 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p9" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('9')" id=AREF>"App expression after windsorizing"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>App expression after windsorizing</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID10 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p10" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('10')" id=AREF>"Discovering shared expression patterns"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Discovering shared expression patterns</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID11 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p11" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('11')" id=AREF>"Transcript neighborhoods"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Transcript neighborhoods</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID12 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p12" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('12')" id=AREF>"App and Atcay transcript scatterplot"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>App and Atcay transcript scatterplot</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID13 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p13" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('13')" id=AREF>"App transcript and eight of..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>App transcript and eight of its neighbors</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID14 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p14" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('14')" id=AREF>App transcript coexpression neighborhood</a></b></font></td> </tr> </table> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID15 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p15" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('15')" id=AREF>"Correlations of App with classical..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Correlations of App with classical traits</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID16 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p16" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('16')" id=AREF>"Network Graph of App with..."</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Network Graph of App with classical traits</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID17 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p17" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('17')" id=AREF>"Summary of Part 1:"</a></b></font></td> </tr> </table> <table> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td colspan=1><font face=Arial size=2>Summary of Part 1:</font></td> </tr> </table> <br> <table width=100%> <tr> <td width=1 ><script> if ( parent.base.isnav ) { document.write('<ilayer id= LAYERID18 VISIBILITY=hidden >></ilayer>'); } </script></td> <td width=100% id="p18" ><font face=Arial size=2><b><a href="javascript:parent.base.Slide('18')" id=AREF>Contact for comments and improvements:</a></b></font></td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_navigation_bar.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_navigation_bar.htm deleted file mode 100755 index f47a3707..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/outline_navigation_bar.htm +++ /dev/null @@ -1,37 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script><script language=JavaScript><!-- - -function restore() { -if( navigator.platform != "MacPPC" ) - self.location.reload(); -} - -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>' ); - } -}//--> -</script> </head> <body background=navbg.gif topmargin=1 onresize="restore()" scroll="no" > <script language=JavaScript><!-- -writebody(); -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_active.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_active.gif deleted file mode 100755 index 004a872f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_active.gif +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_disabled.gif b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_disabled.gif deleted file mode 100755 index 8a467185..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/prev_disabled.gif +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/script.js b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/script.js deleted file mode 100755 index 7c9fb703..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/script.js +++ /dev/null @@ -1,1351 +0,0 @@ -var CtxAlwaysOn = false; -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 - 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( " >   " + 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); 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This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator."); - */ - if ( isFLATFiles <= 0 ) { - /* if ( IsFramesMode() ) - window.alert("This presentation contains content that your browser may not be able to display properly. This presentation is optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); - */ - window.location.replace( "webqtl_demo2_part1.ppt_files/error.htm" ); - } - /* - else if ( IsFramesMode() && !isWebTV() ) - StatusPlay( "This presentation contains content that your browser may not be able to show properly. This presentation was optimized for more recent versions of Microsoft Internet Explorer or Netscape Navigator." ); - */ - jpegArray ( 18 ); - } - -} - -function isWebTV() { - if ( window.navigator.appName.indexOf( 'WebTV' ) >= 0 ) - return true; - return false; -} - -var count; -var statusText; -var statusfirst = 0; - function display50( text ) -{ - len = text.length; - if ( len < 50 && count < 2) { - window.status = text; - window.setTimeout( "repeat()", 300 ); - } - else { - var period = 200; - window.status = text; - newtext = text.substring( 1, len ); - if ( statusfirst ) { - statusfirst = 0; - period = 2000; - } - window.setTimeout( "display50( newtext )", period ); - } -} -function repeat( ) { - count++; - statusfirst = 1; - display50( statusText ); -} - -function StatusPlay( text ) { - count = 0; - statusText = text; - repeat( ); - } -function makeSlide( i, notes, visible ) { - g_notesTable[i] = notes; - g_hiddenSlide[i] = visible; -} - diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.htm deleted file mode 100755 index d17c2490..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: GeneNetwork and WebQTL:"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.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:.88%;left:3.31%;width:84.37%;height:9.89%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='mso-line-spacing:"-277 0 -1";mso-margin-left-alt:232; mso-text-indent-alt:0;position:absolute;top:0%;left:1.25%;width:97.95%; height:100.0%'><span style='font-size:105%'><i>GeneNetwork and WebQTL:</i></span><span style='font-size:68%;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> <div style='position:absolute;top:24.02%;left:5.82%;width:69.0%;height:50.7%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='position:absolute;top:0%;left:2.87%;width:97.12%; height:71.08%'> <div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:0%;left:0%;width:92.68%;height:53.43%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Part 1: How to study </span></span><span style='position:absolute;top:31.19%; left:8.1%;width:91.89%'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>expression variation and </span></span><span style='position:absolute; top:61.46%;left:8.1%;width:91.89%'><span style='font-size:106%;color:#E9EB5D; mso-color-index:3'>covariation (slides 2–16)<br> </span></span></div> <div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56;position:absolute;top:63.23%;left:0%;width:100.0%;height:36.76%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='mso-special-format: nobullet;display:none;color:#FBFDB8;font-family:"Monotype Sorts";font-size: 99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Part 2. Discovering upstream </span></span><span style='position:absolute; top:45.33%;left:7.5%;width:89.32%'><span style='font-size:106%;color:#E9EB5D; mso-color-index:3'>modulators (slides 17–30)</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></span></div> </div> </div> <img border=0 src="slide0001_image001.png" style='position:absolute;top:21.9%; left:74.56%;width:23.57%;height:64.31%'> <div class=O style='position:absolute;top:79.32%;left:75.89%;width:10.46%; height:14.48%'> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:0%;left:0%;width:100.0%;height:42.68%'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17;position:absolute;top:46.34%;left:0%;width:82.27%;height:54.87%'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </div> <div class=O style='position:absolute;top:66.43%;left:3.44%;width:80.66%; height:11.48%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>PowerPoint ÒNormal viewÓ has notes that may be </i></span></span><span style='position:absolute;top:50.76%;left:0%;width:86.53%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>useful companions to these slides.</i></span><span style='font-family: "Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index:3;mso-special-format: lastCR;display:none'><br> </span></span></div> <div class=O style='position:absolute;top:10.95%;left:6.35%;width:55.23%; height:7.42%'><span style='font-family:"Gill Sans";font-size:283%;color:#E9EB5D'><i>a PowerPoint Presentation</i></span><span style='font-family:"Gill Sans"; font-size:317%;color:#E9EB5D;mso-special-format:lastCR;display:none'><i><br> </i></span></div> <div class=O style='position:absolute;top:92.4%;left:75.23%;width:26.49%; height:3.88%'><span style='font-family:Helvetica;font-size:167%;color:#E9EB5D'><i>RWW 07.23.2005</i></span></div> <div class=O style='position:absolute;top:81.97%;left:3.44%;width:77.21%; height:11.48%'> <div style='position:absolute;top:0%;left:0%;width:88.16%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>You can also download this PowerPoint at<br> </i></span></div> <div style='position:absolute;top:50.76%;left:0%;width:100.0%;height:49.23%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'><i>ftp://atlas.utmem.edu/public/webqtl_demo2.ppt </i></span><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Welcome to a short demonstration of the GeneNetwork and its WebQTL module. Please adjust the size of the windows on your monitor so that you can see part of this page, as well as GeneNetwork windows. WebQTL produces a large number of new windows, so you may need to modify your browser preferences to permit pop-ups. In this demonstration, we explore one important transcript expressed in the brain: the amyloid beta precursor protein messenger RNA. A protein product of this mRNA, the APP protein, is associated with AlzheimerÕs disease.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>My thanks to Dr. Robert F. Clark and Wenli Cai for testing this PowerPoint demonstration and making many improvements.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>(Initial version of June 2003 by Rob Williams. Edits July 13, 2005 by RW and RFC. Edit July 14, 2005 by WC. Final edits by RF Clark, July 22, 2005.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_image001.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_image001.png deleted file mode 100755 index a1cb20e4..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_image001.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_notes_pane.htm deleted file mode 100755 index 7c670210..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0001_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Welcome to a short demonstration of the GeneNetwork and its WebQTL module. Please adjust the size of the windows on your monitor so that you can see part of this page, as well as GeneNetwork windows. WebQTL produces a large number of new windows, so you may need to modify your browser preferences to permit pop-ups. In this demonstration, we explore one important transcript expressed in the brain: the amyloid beta precursor protein messenger RNA. A protein product of this mRNA, the APP protein, is associated with AlzheimerÕs disease.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>My thanks to Dr. Robert F. Clark and Wenli Cai for testing this PowerPoint demonstration and making many improvements.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>(Initial version of June 2003 by Rob Williams. Edits July 13, 2005 by RW and RFC. Edit July 14, 2005 by WC. Final edits by RF Clark, July 22, 2005.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002.htm deleted file mode 100755 index 8627e129..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- -gId="slide0002.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//--> -</script><script for=window event=onload language=JavaScript><!-- -if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//--> -</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0002_image002.png" style='position:absolute;top:8.3%; left:.39%;width:86.35%;height:86.21%'><img border=0 src="slide0002_image003.png" style='position:absolute;top:34.27%;left:59.07%;width:12.18%;height:14.48%'> <div style='position:absolute;top:46.64%;left:85.43%;width:16.29%;height:12.01%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:2.94%;left:5.69%;width:93.49%; height:91.17%'> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:0%;left:0%; width:91.3%;height:51.61%'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>Choose<br> </span></div> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:48.38%; left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>database</span></div> </div> </div> <div style='position:absolute;top:62.19%;left:86.62%;width:21.05%;height:12.72%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:6.94%;left:5.03%;width:89.93%; height:86.11%'> <div style='position:absolute;top:0%;left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>Enter<br> </span></div> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:48.38%; left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'><i>APP</i></span><span style='font-family:"Gill Sans";font-size:250%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><i><br> </i></span></div> </div> </div> <div style='position:absolute;top:77.73%;left:85.96%;width:12.58%;height:12.72%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:6.94%;left:8.42%;width:91.57%; height:86.11%'> <div style='position:absolute;top:0%;left:0%;width:91.95%;height:51.61%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>Select<br> </span></div> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:48.38%; left:0%;width:100.0%;height:51.61%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>search</span></div> </div> </div> <div style='position:absolute;top:.88%;left:0%;width:111.92%;height:9.18%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div style='position:absolute;top:0%;left:.94%;width:99.05%;height:80.76%'> <div class=B1 style='mso-margin-left-alt:644;mso-text-indent-alt:420'></div> <div class=B2 style='mso-margin-left-alt:937;mso-text-indent-alt:716'></div> <div class=B3 style='mso-margin-left-alt:1232;mso-text-indent-alt:1009'></div> <div class=B4 style='mso-margin-left-alt:1544;mso-text-indent-alt:1304'></div> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:0;position:absolute;top:0%;left:0%;width:100.0%;height: 100.0%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8; font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size: 106%;color:#E9EB5D;mso-color-index:3'>PART 1: How to study variation and covariation</span></div> </div> </div> <div style='position:absolute;top:15.54%;left:85.82%;width:16.15%;height:22.43%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='mso-line-spacing:"-224 0 0";position:absolute;top:1.57%; left:6.55%;width:94.26%;height:94.48%'><span style='position:absolute; top:0%;left:0%;width:91.3%'><span style='font-family:"Gill Sans";font-size: 217%;color:#E9EB5D;mso-color-index:3'>Choose<span style="mso-spacerun: yes"> </span></span></span><span style='position:absolute;top:25.0%; left:0%;width:91.3%'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>species, </span></span><span style='position: absolute;top:49.16%;left:0%;width:91.3%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>group, </span></span><span style='position:absolute;top:73.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>and type</span></span></div> </div> <img border=0 src="slide0002_image004.png" style='position:absolute;top:71.37%; left:48.87%;width:12.58%;height:13.78%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Please link to the web site:<span style="mso-spacerun: yes"> </span>http://www.genenetwork.org</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>To begin a search you make choices about what species, group, and database to explore.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>For this demonstration enter APP as above and click on the SEARCH button. Make sure that the DEFAULT SETTINGS are species = Mouse, Group = BXD, Type = Whole Brain, and Database = INIA BRAIN mRNA M430 (Apr05) PDNN.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. The GeneNetwork and WebQTL are often used to work with public data sets. However, it is possible to enter and analyze your own data for specific genetic reference populations such as the BXD genetic reference population of mice or the HXB strains of rat. Entering your own data is a more advanced topic, but if you click on the HOME pop-down menu (upper left), you will see ÒEnter Trait DataÓ that will explain the process.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>2.</font><font face=Helvetica size=3> For help on advanced searching methods read the left side of the page (INTRODUCTION).<span style="mso-spacerun: yes"> </span>If you make a search term too complex, you may get no hits (try entering Òamyloid betaÓ for example). If you make it too simple, you may also get too many.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>3.</font><font face=Helvetica size=3> Use the asterisk * as a wildcard. For example, to find all <i>Hoxb</i> transcripts, search for Hoxb*.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>4.</font><font face=Helvetica size=3> In some cases you can also research for transcripts and genes using special search strings such as Ò</font><font face=Geneva size=3>Mb = (Chr1, 100 102)Ó to find all genes on Chromosome 1 between 98 and 104 megabases (donÕt actually use the quotes). Details are described at </font><font face=Verdana size=3>http://www.genenetwork.org/searchHelp.html</font><font face=Geneva size=3>.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>5.<span style="mso-spacerun: yes"> </span>These INFO buttons provide links to data about the different data types. Try them.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>6.<span style="mso-spacerun: yes"> </span>The SET TO DEFAULT button is used to change the database default setting to match your typical search categories.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png deleted file mode 100755 index 2eb797be..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image002.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png deleted file mode 100755 index d1370484..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image003.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png deleted file mode 100755 index a4f088b8..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_image004.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm deleted file mode 100755 index 5f7740c5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0002_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Please link to the web site:<span style="mso-spacerun: yes"> </span>http://www.genenetwork.org</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>To begin a search you make choices about what species, group, and database to explore.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>For this demonstration enter APP as above and click on the SEARCH button. Make sure that the DEFAULT SETTINGS are species = Mouse, Group = BXD, Type = Whole Brain, and Database = INIA BRAIN mRNA M430 (Apr05) PDNN.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. The GeneNetwork and WebQTL are often used to work with public data sets. However, it is possible to enter and analyze your own data for specific genetic reference populations such as the BXD genetic reference population of mice or the HXB strains of rat. Entering your own data is a more advanced topic, but if you click on the HOME pop-down menu (upper left), you will see ÒEnter Trait DataÓ that will explain the process.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>2.</font><font face=Helvetica size=2> For help on advanced searching methods read the left side of the page (INTRODUCTION).<span style="mso-spacerun: yes"> </span>If you make a search term too complex, you may get no hits (try entering Òamyloid betaÓ for example). If you make it too simple, you may also get too many.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>3.</font><font face=Helvetica size=2> Use the asterisk * as a wildcard. For example, to find all <i>Hoxb</i> transcripts, search for Hoxb*.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>4.</font><font face=Helvetica size=2> In some cases you can also research for transcripts and genes using special search strings such as Ò</font><font face=Geneva color="#222222" size=2>Mb = (Chr1, 100 102)Ó to find all genes on Chromosome 1 between 98 and 104 megabases (donÕt actually use the quotes). Details are described at </font><font face=Verdana color=black size=2>http://www.genenetwork.org/searchHelp.html</font><font face=Geneva color="#222222" size=2>.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>5.<span style="mso-spacerun: yes"> </span>These INFO buttons provide links to data about the different data types. Try them.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>6.<span style="mso-spacerun: yes"> </span>The SET TO DEFAULT button is used to change the database default setting to match your typical search categories.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003.htm deleted file mode 100755 index 5507bd68..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.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.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0003_image005.png" style='position:absolute;top:34.27%; left:59.07%;width:12.18%;height:14.48%'> <div style='position:absolute;top:.88%;left:.79%;width:105.69%;height:9.18%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div style='position:absolute;top:0%;left:1.0%;width:98.99%;height:80.76%'> <div class=B1 style='mso-margin-left-alt:644;mso-text-indent-alt:420'></div> <div class=B2 style='mso-margin-left-alt:937;mso-text-indent-alt:716'></div> <div class=B3 style='mso-margin-left-alt:1232;mso-text-indent-alt:1009'></div> <div class=B4 style='mso-margin-left-alt:1544;mso-text-indent-alt:1304'></div> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:0;position:absolute;top:0%;left:0%;width:100.0%;height: 100.0%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8; font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size: 106%;color:#E9EB5D;mso-color-index:3'>Please also use the Glossary, FAQ, and News</span></div> </div> </div> <img border=0 src="slide0003_image006.png" style='position:absolute;top:10.07%; left:1.72%;width:69.66%;height:60.95%'><img border=0 src="slide0003_image008.png" style='position:absolute;top:9.18%;left:18.8%; width:12.58%;height:13.78%'><img border=0 src="slide0003_image009.png" style='position:absolute;top:49.11%;left:38.27%;width:60.0%;height:48.58%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>SHORT DETOUR to the HELP menu. If you are new to the GeneNetwork, you may find it helpful to review the The Glossary and FAQ pages shown above. We are in the process of making ÒliveÓ demos for some of the key modules in the GeneNetwork. Check the NEWS every month or two to find out about new features.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png deleted file mode 100755 index d1370484..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image005.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image006.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image006.png deleted file mode 100755 index c9843a48..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image006.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image008.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image008.png deleted file mode 100755 index 504177df..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image008.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image009.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image009.png deleted file mode 100755 index 901c77a0..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_image009.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm deleted file mode 100755 index b8742fdc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0003_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>SHORT DETOUR to the HELP menu. If you are new to the GeneNetwork, you may find it helpful to review the The Glossary and FAQ pages shown above. We are in the process of making ÒliveÓ demos for some of the key modules in the GeneNetwork. Check the NEWS every month or two to find out about new features.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004.htm deleted file mode 100755 index ab2d96f6..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: Search results"> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.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.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0004_image010.png" style='position:absolute;top:9.18%; left:3.31%;width:68.74%;height:90.81%'><img border=0 src="slide0004_image012.png" style='position:absolute;top:63.78%;left:63.57%; width:14.7%;height:6.53%'> <div class=O style='position:absolute;top:45.93%;left:80.13%;width:18.94%; height:47.17%'> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:0%;left:0%; width:100.0%;height:44.94%'><span style='position:absolute;top:0%;left:0%; width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>Highlight </span></span><span style='position:absolute; top:24.16%;left:0%;width:100.0%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>this probe </span></span><span style='position:absolute;top:49.16%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>set in red </span></span><span style='position:absolute;top:73.33%; left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>and</span><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3;display:none'><i><br> </i></span></span></div> <div style='mso-line-spacing:"-224 0 0";position:absolute;top:43.82%; left:0%;width:100.0%;height:56.17%'><span style='position:absolute;top:0%; left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>click. You </span></span><span style='position:absolute;top:20.0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>do NOT </span></span><span style='position:absolute;top:39.33%;left:0%; width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D; mso-color-index:3'>have to </span></span><span style='position:absolute; top:59.33%;left:0%;width:100.0%'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>select the </span></span><span style='position:absolute;top:78.66%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3'>checkbox</span><span style='font-family:"Gill Sans";font-size:250%; color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR;display:none'><br> </span></span></div> </div> <div style='position:absolute;top:-4.41%;left:1.72%;width:84.63%;height:18.19%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=T style='position:absolute;top:29.12%;left:1.4%;width:97.18%; height:42.71%'><span style='font-size:82%'>Search results</span><span style='mso-special-format:lastCR;display:none'><br> </span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>RESULTS OF THE APP SEARCH.<span style="mso-spacerun: yes"> </span>A search of the INIA Brain database generates 18 matches, 10 of which are shown above. The GeneNetwork will display several hundred matches in pages of 40 each. If a search generates a larger numbers of hits, then you will need to refine search terms.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. APP is a great transcript to introduce you to the complexity and power of new array platforms that often provide ÒalternativeÓ expression estimates for single genes. There are seven probe sets that target different parts of the APP transcript. Which of the alternative measurements is most appropriate and informative? Have a look at the FAQ page for more on this topic, but general advice: 1. be skeptical and try to validate that the correct transcript and gene is being measured; 2. check what part of the transcript is complementary to the probes; 3. evaluate the performance of individual probes based on expression level, signal-to-noise and other error terms such as the standard deviation and error.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. In this particular case we have highlighted and selected # 5 on this SEARCH RESULTS page. The annotation for this probe set mentions that it targets the last three exons and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span style="mso-spacerun: yes"> </span>That is just what we want.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. Most probe sets have not been annotated in as much detail as App. Refer tot the FAQ to learn how to annotate probe sets yourself.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png deleted file mode 100755 index 08c136e3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image010.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png deleted file mode 100755 index b8e67f4d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_image012.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm deleted file mode 100755 index f7336dcc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0004_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>RESULTS OF THE APP SEARCH.<span style="mso-spacerun: yes"> </span>A search of the INIA Brain database generates 18 matches, 10 of which are shown above. The GeneNetwork will display several hundred matches in pages of 40 each. If a search generates a larger numbers of hits, then you will need to refine search terms.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. APP is a great transcript to introduce you to the complexity and power of new array platforms that often provide ÒalternativeÓ expression estimates for single genes. There are seven probe sets that target different parts of the APP transcript. Which of the alternative measurements is most appropriate and informative? Have a look at the FAQ page for more on this topic, but general advice: 1. be skeptical and try to validate that the correct transcript and gene is being measured; 2. check what part of the transcript is complementary to the probes; 3. evaluate the performance of individual probes based on expression level, signal-to-noise and other error terms such as the standard deviation and error.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. In this particular case we have highlighted and selected # 5 on this SEARCH RESULTS page. The annotation for this probe set mentions that it targets the last three exons and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span style="mso-spacerun: yes"> </span>That is just what we want.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. Most probe sets have not been annotated in as much detail as App. Refer tot the FAQ to learn how to annotate probe sets yourself.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005.htm deleted file mode 100755 index 53f61532..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- -gId="slide0005.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//--> -</script><script for=window event=onload language=JavaScript><!-- -if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//--> -</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'><img border=0 src="slide0005_image013.png" style='position:absolute;top:8.83%; left:2.51%;width:77.48%;height:80.56%'> <div style='position:absolute;top:1.06%;left:0%;width:108.21%;height:8.3%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:1.83%;width:98.16%; height:78.72%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>First page of data: The Trait Data and Analysis Form</span><span style='font-size:106%;color:#E9EB5D; mso-color-index:3;mso-special-format:lastCR;display:none'><br> </span></div> </div> <img border=0 src="slide0005_image014.png" style='position:absolute;top:34.98%; left:68.74%;width:16.42%;height:9.71%'> <div style='position:absolute;top:23.32%;left:84.76%;width:16.68%;height:34.09%; filter:DropShadow(Color=#000000, OffX=2, OffY=2)'> <div class=O style='position:absolute;top:2.07%;left:6.34%;width:93.65%; height:95.33%'><span style='position:absolute;top:0%;left:0%;width:90.67%'><span style='font-size:200%;color:#E9EB5D'><i>Click </i></span></span><span style='position:absolute;top:16.3%;left:0%;width:90.67%'><span style='font-size:200%;color:#E9EB5D'><i>here<br> </i></span></span> <div style='position:absolute;top:33.15%;left:0%;width:100.0%;height:16.84%'><span style='font-size:200%;color:#E9EB5D'><i>to learn<br> </i></span></div> <div style='position:absolute;top:49.45%;left:0%;width:90.67%;height:16.84%'><span style='font-size:200%;color:#E9EB5D'><i>about<br> </i></span></div> <div style='position:absolute;top:66.3%;left:0%;width:90.67%;height:16.84%'><span style='font-size:200%;color:#E9EB5D'><i>data<br> </i></span></div> <div style='position:absolute;top:83.15%;left:0%;width:90.67%;height:16.84%'><span style='font-size:200%;color:#E9EB5D'><i>source</i></span></div> </div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Trait Data and Analysis Form is the single most important page from the point of view of working with GeneNetwork data. Please read the text carefully. Explore the links, but do not close this page. We will need it many more times in this demonstration.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. What is this database? It is called INIA Brain mRNA M430 (Apr05) PDNN, but what does that actually mean. How much of the brain was used? How were the animals processed? Most of these types of questions can be answered by clicking on the DATABASE link.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. Transcript/gene LOCATION data is usually from the most recent assembly. You can VERIFY the location of the probes and probe set using the two VERIFY buttons. VERIFY UCSC performs a sequence alignment (BLAT analysis) of the probes to the most recent assembly.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. The PROBE TOOL button provides you with highly detailed information on the probe sequences used to assemble the probe set. For example, in this case you can find out which probes correspond to which of the three exons. You can also review the performance of the individual probes. Please check the GLOSSARY for additional details on probes.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. The identifiers (IDs) provide links to other key resources.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png deleted file mode 100755 index 55769e36..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image013.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png deleted file mode 100755 index e49ba16e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_image014.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm deleted file mode 100755 index fbe8c631..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0005_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The Trait Data and Analysis Form is the single most important page from the point of view of working with GeneNetwork data. Please read the text carefully. Explore the links, but do not close this page. We will need it many more times in this demonstration.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. What is this database? It is called INIA Brain mRNA M430 (Apr05) PDNN, but what does that actually mean. How much of the brain was used? How were the animals processed? Most of these types of questions can be answered by clicking on the DATABASE link.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. Transcript/gene LOCATION data is usually from the most recent assembly. You can VERIFY the location of the probes and probe set using the two VERIFY buttons. VERIFY UCSC performs a sequence alignment (BLAT analysis) of the probes to the most recent assembly.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. The PROBE TOOL button provides you with highly detailed information on the probe sequences used to assemble the probe set. For example, in this case you can find out which probes correspond to which of the three exons. You can also review the performance of the individual probes. Please check the GLOSSARY for additional details on probes.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>4. The identifiers (IDs) provide links to other key resources.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006.htm deleted file mode 100755 index fa44d20c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- -gId="slide0006.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//--> -</script><script for=window event=onload language=JavaScript><!-- -if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//--> -</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-1.06%;left:0%;width:100.26%;height:10.07%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:1.98%;width:96.82%; height:73.68%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Data sources: Metadata for each resource</span></div> </div> <img border=0 src="slide0006_image015.png" style='position:absolute;top:6.71%; left:3.31%;width:60.39%;height:92.22%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Most of the database components and resources in The GeneNetwork are linked to metadata pages that provide a human-readable summary of how, why, where, when, and with whom the data were generated. Before you get too involved with a data set, it is naturally important to read this information. While the data in The GeneNetwork may be accessible and useful, that does not always mean that the data is public domain and available for you to use in publication or for profit purposes. If you want to know more about the data ownership and usage, please read through the POLICIES pop-down menu items.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png deleted file mode 100755 index ff7d776a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_image015.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm deleted file mode 100755 index f29819ad..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0006_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Most of the database components and resources in The GeneNetwork are linked to metadata pages that provide a human-readable summary of how, why, where, when, and with whom the data were generated. Before you get too involved with a data set, it is naturally important to read this information. While the data in The GeneNetwork may be accessible and useful, that does not always mean that the data is public domain and available for you to use in publication or for profit purposes. If you want to know more about the data ownership and usage, please read through the POLICIES pop-down menu items.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007.htm deleted file mode 100755 index a30b21f1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- -gId="slide0007.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//--> -</script><script for=window event=onload language=JavaScript><!-- -if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//--> -</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:-.35%;left:-.79%;width:109.13%;height:7.42%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:1.82%;width:98.17%; height:88.09%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'>Expression estimates for </span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3'> on the Trait Data form</span><span style='font-size:81%;color:#E9EB5D;mso-color-index:3'> </span></div> </div> <div style='position:absolute;top:81.09%;left:2.51%;width:110.46%;height:11.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:7.69%;left:.83%;width:99.16%; height:84.61%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:183%;color:#E9EB5D;mso-color-index: 3'>Trait data for each strain with SE when known. For array data the scale is </span></span><span style='position:absolute;top:49.09%;left:0%;width:84.28%'><span style='font-family:"Gill Sans";font-size:183%;color:#E9EB5D;mso-color-index: 3'>~ log base 2.<span style="mso-spacerun: yes"> </span></span><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>F1 data = 16.723 = 2^16.723 = 108,174</span></span></div> </div> <img border=0 src="slide0007_image016.png" style='position:absolute;top:7.77%; left:2.51%;width:51.65%;height:72.26%'><img border=0 src="slide0007_image017.png" style='position:absolute;top:33.92%;left:57.88%; width:30.72%;height:13.42%'> <div style='position:absolute;top:47.7%;left:57.48%;width:36.29%;height:18.9%; filter:DropShadow(Color=#000000, OffX=2, OffY=1)'> <div class=O style='position:absolute;top:3.73%;left:2.91%;width:97.08%; height:96.26%'><span style='position:absolute;top:0%;left:0%;width:96.24%'><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>These values can all </span></span><span style='position:absolute;top:25.24%;left:0%;width:93.98%'><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>be changed by the </span></span><span style='position:absolute;top:49.51%;left:0%;width:100.0%'><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>user. (Yes, there is a </span></span><span style='position:absolute;top:74.75%;left:0%;width:93.98%'><span style='font-size:167%;color:#E9EB5D;mso-color-index:3'>RESET)</span></span></div> </div> </div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>This slide shows you the lower parts of the Trait Data and Analysis Form with the data for the first set of BXD strains</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image016.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image016.png deleted file mode 100755 index 53a17c76..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image016.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image017.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image017.png deleted file mode 100755 index 308c4df0..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_image017.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_notes_pane.htm deleted file mode 100755 index f5bc813e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0007_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>This slide shows you the lower parts of the Trait Data and Analysis Form with the data for the first set of BXD strains</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008.htm deleted file mode 100755 index c0fa9166..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- -gId="slide0008.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//--> -</script><script for=window event=onload language=JavaScript><!-- -if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//--> -</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:.53%;left:.79%;width:98.54%;height:8.12%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:2.01%;width:96.9%; height:91.3%'><span style='mso-special-format:nobullet;display:none;color:#FBFDB8; font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size: 106%;color:#E9EB5D;mso-color-index:3'>Critiquing the </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> data the Trait Data</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div style='position:absolute;top:74.38%;left:2.51%;width:110.86%;height:13.78%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=O style='position:absolute;top:6.41%;left:.83%;width:99.16%; height:88.46%'><span style='position:absolute;top:0%;left:0%;width:98.55%'><span style='font-family:"Gill Sans";font-size:150%;color:#E9EB5D;mso-color-index: 3'>Use the BASIC STATISTICS button to evaluate the App data. You will find that App data </span></span><span style='position:absolute;top:31.88%;left:0%; width:100.0%'><span style='font-family:"Gill Sans";font-size:150%;color:#E9EB5D; mso-color-index:3'>from the different strains are not equally trustworthy. BXD8 is an obvious outlier without </span></span><span style='position:absolute; top:63.76%;left:0%;width:93.85%'><span style='font-family:"Gill Sans"; font-size:150%;color:#E9EB5D;mso-color-index:3'>replication (no error bar)</span><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'>. BXD33 is also suspiciously low. BXD5 is noisy. </span><span style='font-family:"Gill Sans"; font-size:150%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></span></div> </div> <img border=0 src="slide0008_image018.png" style='position:absolute;top:7.77%; left:2.11%;width:16.02%;height:18.72%'><img border=0 src="slide0008_image019.png" style='position:absolute;top:8.3%;left:18.27%; width:73.37%;height:66.07%'><img border=0 src="slide0008_image021.png" style='position:absolute;top:87.27%;left:59.6%;width:30.72%;height:13.42%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The Basic Statistics page allows you to evaluate some aspects of the data quality. In this case, BXD8 is a potential problem. An outlier of this type may be generated by a technical artifact (bad sample?). However, it is also possible that BXD8 just has genuine low endogenous expression of App and may therefore be a particularly valuable model for research. There are different ways to treat problematic data of these types. One way is simply to discard this datum. The other way is to prevent outliers from have too much influence quantitatively, while leaving them in their low (or high positions). This is called windsorizing the data (after King Henry the VIII who had a habit of chopping heads). In this case, we have windsorized the BXD8 to a value of 16.0 and the BXD33 to a value of 16.02. Rank is retained. We are making a bet that the two lowest strains are really low, but we are hedging our bet and just making them a little lower than BXD90. This removes their ÒundueÓ influence.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. It turns out that BXD8 is a strain with many odd phenotypes. The whole strain is essentially an outlier for many traits. Therefore, the low App expression data may be quite accurate. Still, it would be comforting to have at least two more replicates.</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image018.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image018.png deleted file mode 100755 index 9535e6bb..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image018.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image019.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image019.png deleted file mode 100755 index 7e86d735..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image019.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image021.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image021.png deleted file mode 100755 index 2f8dfb0a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_image021.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm deleted file mode 100755 index 455928c7..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0008_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The Basic Statistics page allows you to evaluate some aspects of the data quality. In this case, BXD8 is a potential problem. An outlier of this type may be generated by a technical artifact (bad sample?). However, it is also possible that BXD8 just has genuine low endogenous expression of App and may therefore be a particularly valuable model for research. There are different ways to treat problematic data of these types. One way is simply to discard this datum. The other way is to prevent outliers from have too much influence quantitatively, while leaving them in their low (or high positions). This is called windsorizing the data (after King Henry the VIII who had a habit of chopping heads). In this case, we have windsorized the BXD8 to a value of 16.0 and the BXD33 to a value of 16.02. Rank is retained. We are making a bet that the two lowest strains are really low, but we are hedging our bet and just making them a little lower than BXD90. This removes their ÒundueÓ influence.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>1. It turns out that BXD8 is a strain with many odd phenotypes. The whole strain is essentially an outlier for many traits. Therefore, the low App expression data may be quite accurate. Still, it would be comforting to have at least two more replicates.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009.htm deleted file mode 100755 index 2daff7ac..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.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.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 deleted file mode 100755 index e03c35ed..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_image022.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_notes_pane.htm deleted file mode 100755 index b2f9f9f2..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0009_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Now we get a much better feel for the variation in the error among the cases. Those without error bars are of course the ÒnoisiestÓ of all. This data set is not complete yet (the aim is to acquire at least one male-female sample for each BXD strain).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010.htm deleted file mode 100755 index 4d02c34e..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.sld {left:0px !important; width:6.0in !important; height:4.5in !important; font-size:76% !important;} --> </style> <script language=JavaScript src=script.js></script><script language=JavaScript><!-- -gId="slide0010.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: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 deleted file mode 100755 index 1d32d035..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image023.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image024.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image024.png deleted file mode 100755 index 152e5045..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_image024.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_notes_pane.htm deleted file mode 100755 index 3d3f0e48..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0010_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Finally, we can now start an analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>We ask a simple question:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Do differences in this particular App transcript steady-state abundance level correlate with those of any other transcripts in the same INIA Brain mRNA M430 data set?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>You can CHOOSE many other DATABASES at this point if you want, but for now letÕs stick with the default.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. There are different ways to sort the correlations. The most obvious is by p-value (most significant values at the top of the list), but it is also interesting to sort the top 100 or top 500 by their gene symbol (gene ID) or by their chromosomal location (position).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. If you donÕt want your analysis to be sensitive to outliers, then you may want to choose to use the Spearman Rank Order method of calculating correlations.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011.htm deleted file mode 100755 index 362057fc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <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="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 deleted file mode 100755 index d29a333f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_image025.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm deleted file mode 100755 index 1f0dd0d1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0011_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>The Traits Correlation output window (Correlation Results) compares App expression data with all other traits in this INIA Brain data set. The most significant 100 or 500 transcripts are sorted by their p-values. The top correlation is that of the probe set to itself (often a value of 1.0, but in this case we modified the App values manually by windsorizing the data). The next best correlation is to another App probe set. The fourth correlation is interesting and suggests that there may be a link between App and a particular type of ataxia (Atcay).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>Use the checkboxes to the far left to select traits that you want to study together. Once you have selected interesting traits, click on the ADD SELECTION button. This puts all of the selected traits into a SELECTIONS WINDOW for other types of analysis.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. The p-value is not corrected for multiple tests. A conservative approach for array data would be to assume 10,000 nominally independent tests. Subtract 4 from the exponent and if the value is still smaller than 0.05 you may have a real correlation.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. The LITERATURE CORRELATION is a data type generated by Drs. Ramin Homayouni and Michael Berry. Click on the header column by the asterisk for more information on this highly useful data type.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>4. We are using Pearson product moment correlations rather that the Spearman rank order correlation. But you can select either in the previous step.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012.htm deleted file mode 100755 index 4f1cf425..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <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="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 deleted file mode 100755 index a0675ffc..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_image026.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_notes_pane.htm deleted file mode 100755 index c13d07ec..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0012_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>By clicking on the CORRELATION of the Atcay transcript to the App transcript, you can generate a Correlation plot between these two transcripts. In this App and Atcay scatterplot, each point is a strain mean value. For example, BXD33 and BXD8 have low App and Atcay expressions. The two parental strains and the F1 are also included in this plot.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013.htm deleted file mode 100755 index 5aa623bf..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.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; -//--> -</script><script for=window event=onload language=JavaScript><!-- -if( !IsSldOrNts() ) return; -if( MakeNotesVis() ) return; -LoadSld( gId ); -playList();MakeSldVis(1); -//--> -</script> </head> <body style='margin:0px;background-color:black' onclick="DocumentOnClick(event)" onresize="_RSW()" onkeypress="_KPH(event)"> <div id=SlideObj class=sld style='position:absolute;top:0px;left:0px; width:755px;height:566px;font-size:16px;background-color:#484848;clip:rect(0%, 101%, 101%, 0%); visibility:hidden'><img src="master03_background.png" v:shapes="_x0000_s1026" style='position:absolute;top:0%;left:0%;width:100.0%;height:100.0%'> <div style='position:absolute;top:.35%;left:.79%;width:99.47%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:348; mso-text-indent-alt:56;position:absolute;top:0%;left:1.99%;width:96.8%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript and eight of its neighbors</span></div> </div> <img border=0 src="slide0013_image027.png" style='position:absolute;top:9.71%; left:2.51%;width:83.84%;height:90.1%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>A group of traits from many different databases can be selected and brought together for joint analysis. In this case all of the content of the BXD SELECTIONS is from a single BRAIN database, the top 20 neighbors of the App transcript from the Correlation Results table. Eight of these neighbors plus App is shown in the slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>All of items in the BXD SELECTIONS were selected using the SELECT ALL button</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. The buttons at the top (and bottom) of this page can do some cool stuff. We will work with NETWORK GRAPH first.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. Think of the SELECTIONS as your shopping cart. You go to different aisles in the supermarket to acquire different types of items of interest. These could include transcripts, classical phenotypes (longevity, brain weight, prepulse inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves doing some analysis with the items in the cart.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. Different tools handle different numbers of items. Most will handle up to 100 traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_image027.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_image027.png deleted file mode 100755 index ba473846..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_image027.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm deleted file mode 100755 index 4d56b194..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0013_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>A group of traits from many different databases can be selected and brought together for joint analysis. In this case all of the content of the BXD SELECTIONS is from a single BRAIN database, the top 20 neighbors of the App transcript from the Correlation Results table. Eight of these neighbors plus App is shown in the slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>All of items in the BXD SELECTIONS were selected using the SELECT ALL button</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. The buttons at the top (and bottom) of this page can do some cool stuff. We will work with NETWORK GRAPH first.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. Think of the SELECTIONS as your shopping cart. You go to different aisles in the supermarket to acquire different types of items of interest. These could include transcripts, classical phenotypes (longevity, brain weight, prepulse inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves doing some analysis with the items in the cart.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>4. Different tools handle different numbers of items. Most will handle up to 100 traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014.htm deleted file mode 100755 index 156a5132..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: App transcript coexpression neighborhood"> <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"> </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 deleted file mode 100755 index 8f560834..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image029.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image031.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image031.png deleted file mode 100755 index 8d72b4c1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image031.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image033.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image033.png deleted file mode 100755 index c1cd1c01..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_image033.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm deleted file mode 100755 index 728a1a82..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0014_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Output of the Network Graph. Warm colors (orange and red) are positive correlations above 0.5 whereas cool colors (green and blue) are negative correlations. Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2> All of the nodes (gene/transcripts) on this graph are clickable.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. For this graph the App expression values have ÒrevertedÓ to their pre-Windsorized values.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>3. To generate this graph, we used the default setting:<span style="mso-spacerun: yes"> </span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use curved lines (aka ÒedgesÓ).</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015.htm deleted file mode 100755 index c2a26be3..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content=Aug-15-05> <link rel=Stylesheet href="master03_stylesheet.css"> <style media=print> <!--.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 deleted file mode 100755 index dafa2898..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image034.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image035.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image035.png deleted file mode 100755 index 35566d47..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_image035.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm deleted file mode 100755 index 373646fe..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0015_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Going back to the Trait Data and Analysis Form window, we have computed the correlations between strain variation in App expression level and other classical phenotypes that have already been measured in many of the same BXD strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=2>1.</font><font face=Helvetica size=2>The number of common strains varies widely--in this case from 14 to 23 strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>2. We can add these traits (four are selected) to our BXD SELECTIONS window.</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016.htm deleted file mode 100755 index 9432ca4c..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <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="slide0016.htm" -if ( !parent.base.g_done && (parent.base.msie < 0 ) ) { - parent.base.g_done = 1; - document.location.replace( parent.base.GetHrefObj(parent.base.g_currentSlide).m_slideHref); -} -if( !IsNts() ) Redirect( "PPTSld", gId ); -var g_hasTrans = true, g_autoTrans = false, g_transSecs = 1; -//--> -</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:99.47%;height:10.24%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292; mso-text-indent-alt:0;position:absolute;top:0%;left:1.06%;width:98.66%; height:72.41%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Network Graph of </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> with classical traits</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </div> <img border=0 src="slide0016_image036.png" style='position:absolute;top:8.3%; left:3.31%;width:88.21%;height:90.63%'></div> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>We have computed the Network Graph, now using other types of traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Saline Hot Plate Latency is the green node labeled 10020.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Freezing (fear) is the green node labeled 10447.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> </table> </div> <script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_image036.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_image036.png deleted file mode 100755 index baa1d807..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_image036.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_notes_pane.htm deleted file mode 100755 index c2a078c5..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0016_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> </head> <body bgcolor=black text=white> <table border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>We have computed the Network Graph, now using other types of traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Saline Hot Plate Latency is the green node labeled 10020.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Freezing (fear) is the green node labeled 10447.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=2>Notes:</font><br> </td> </tr> </table> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0017.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0017.htm deleted file mode 100755 index afb498b8..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0017.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <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="slide0017.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:1.41%;left:3.31%;width:93.64%;height:14.48%; filter:DropShadow(Color=#000000, OffX=1, OffY=1)'> <div class=B style='mso-line-spacing:"-220 0 -216";mso-margin-left-alt:292; mso-text-indent-alt:0;position:absolute;top:0%;left:1.13%;width:97.59%; height:51.21%'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 1:</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </div> <div style='position:absolute;top:10.77%;left:8.47%;width:100.79%;height:47.87%'> <div class=O1 style='mso-margin-left-alt:432'></div> <div class=O2 style='mso-margin-left-alt:720'></div> <div class=O3 style='mso-margin-left-alt:1008'></div> <div class=O4 style='mso-margin-left-alt:1296'></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:0%; left:0%;width:90.14%;height:11.07%'><span style='position:absolute;top:0%; left:2.76%;width:97.23%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.84%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You have learned the basics about searching for traits<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:11.43%; left:0%;width:84.88%;height:11.07%'><span style='position:absolute;top:0%; left:2.94%;width:97.05%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-3.03%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know some methods to check data quality<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:22.5%; left:0%;width:84.88%;height:11.07%'><span style='position:absolute;top:0%; left:2.94%;width:97.05%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-3.03%;font-family:Arial'>3.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to edit bad or suspicious data<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:33.57%; left:0%;width:90.01%;height:11.07%'><span style='position:absolute;top:0%; left:2.77%;width:97.22%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.85%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to review the basic statistics of a trait<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:44.64%; left:0%;width:93.56%;height:22.14%'><span style='position:absolute;top:0%; left:2.66%;width:97.33%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.74%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a scattergram between two </span></span><span style='position:absolute; top:50.0%;left:2.66%;width:88.06%'><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D;mso-color-index:3'>traits using the Traits Correlation tool<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:66.78%; left:0%;width:100.0%;height:11.07%'><span style='position:absolute;top:0%; left:2.49%;width:97.5%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.56%;font-family:Arial'>6.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to add items to your SELECTIONS window<br> </span></span></div> <div class=O style='mso-margin-left-alt:144;position:absolute;top:77.85%; left:0%;width:99.34%;height:22.14%'><span style='position:absolute;top:0%; left:2.51%;width:97.48%'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:"numbullet3\,1"; position:absolute;left:-2.57%;font-family:Arial'>7.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a Network Graph of traits that </span></span><span style='position:absolute; top:51.66%;left:2.51%;width:82.93%'><span style='font-family:"Gill Sans"; font-size:200%;color:#E9EB5D;mso-color-index:3'>co-vary. </span></span></div> </div> <div class=O style='position:absolute;top:67.31%;left:5.96%;width:105.29%; height:26.5%'><span style='position:absolute;top:0%;left:0%;width:100.0%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'>What does genetic covariance mean? The genetic covariance can </span></span><span style='position:absolute;top:20.0%;left:0%;width:96.1%'><span style='font-family: "Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index:3'>be functional and mechanistic, but it can also be due to linkage </span></span><span style='position:absolute;top:40.0%;left:0%;width:95.97%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'>disequilibrium. Finally, it can be due to sampling error or poor </span></span><span style='position:absolute;top:60.66%;left:0%;width:87.92%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'>experimental design. Evaluate the biological plausibility of </span></span><span style='position:absolute;top:80.66%;left:0%;width:85.28%'><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'>correlations. Test and be skeptical.</span></span></div> </div> <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/slide0018.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018.htm deleted file mode 100755 index e1ee283b..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018.htm +++ /dev/null @@ -1,25 +0,0 @@ -<html> <head> <meta http-equiv=Content-Type content="text/html; charset=macintosh"> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <link id=Main-File rel=Main-File href="webqtl_demo2_part1.ppt.htm"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: 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="slide0018.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: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><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image037.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image037.png deleted file mode 100755 index a1cb20e4..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image037.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image038.png b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image038.png deleted file mode 100755 index e06bd0db..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_image038.png +++ /dev/null Binary files differdiff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_notes_pane.htm deleted file mode 100755 index e2cb435a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0018_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 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=Verdana size=2>END</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/slide0019.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019.htm deleted file mode 100755 index e6b8658d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019.htm +++ /dev/null @@ -1,153 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: GeneNetwork and WebQTL:"> <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("slide0019.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0 * g_height; myleft = 0.03 * g_width; myheight = 0.09 * g_height; mywidth = 0.84 * 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 = 0.09 * 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%;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'><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> </layer></div> </layer><script> - mytop = 0.24 * g_height; myleft = 0.05 * g_width; myheight = 0.5 * g_height; mywidth = 0.69 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.36 * g_height; mywidth = 0.67 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8;font-size:213%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.19 * g_height; mywidth = 0.62 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.62 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Part 1: How to study </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.57 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>expression variation and </span></span></layer><script> - mytop = 0.11 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.57 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>covariation (slides 2–16)<br> </span></span></layer></div> </layer><script> - mytop = 0.22 * g_height; myleft = 0 * g_width; myheight = 0.13 * g_height; mywidth = 0.67 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-256 0 -216";mso-margin-left-alt:348;mso-text-indent-alt: 56'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.67 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); 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Discovering upstream </span></span></layer><script> - mytop = 0.06 * g_height; myleft = 0.05 * g_width; myheight = 0.07 * g_height; mywidth = 0.59 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:106%;color:#E9EB5D;mso-color-index: 3'>modulators (slides 17–30)</span><span style='font-size:94%;color:#E9EB5D; mso-color-index:3;mso-special-format:lastCR;display:none'><br> </span></span></layer></div> </layer></div> </layer></div> </layer><script> - mytop = 0.21 * g_height; myleft = 0.74 * g_width; myheight = 0.64 * g_height; mywidth = 0.23 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.74 * g_width; -yy = 0.21 * g_height; -ht = 0.64 * g_height; -wd = 0.23 * g_width; -document.write( -'<img border=0 src="slide0001_image001.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.79 * g_height; myleft = 0.75 * g_width; myheight = 0.14 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.06 * g_height; mywidth = 0.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:233%;color:#6E6E6E'>RNA</span><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; display:none'><br> </span></div> </layer><script> - mytop = 0.06 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-346 0 0";mso-margin-left-alt:17;mso-text-indent-alt: 17'><span style='font-family:"Arial Rounded MT Bold";font-size:300%;color:#6E6E6E; mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer><script> - mytop = 0.66 * g_height; myleft = 0.03 * g_width; myheight = 0.11 * g_height; mywidth = 0.8 * 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 = 0.8 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'><i>PowerPoint ÒNormal viewÓ has notes that may be </i></span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.69 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'><i>useful companions to these slides.</i></span><span style='font-family:"Gill Sans";font-size:217%;color:#E9EB5D;mso-color-index: 3;mso-special-format:lastCR;display:none'><br> </span></span></layer></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.06 * g_width; myheight = 0.07 * g_height; mywidth = 0.55 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><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> </layer><script> - mytop = 0.92 * g_height; myleft = 0.75 * g_width; myheight = 0.03 * g_height; mywidth = 0.26 * 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:Helvetica;font-size:167%; color:#E9EB5D'><i>RWW 07.23.2005</i></span></div> </layer><script> - mytop = 0.81 * g_height; myleft = 0.03 * g_width; myheight = 0.11 * g_height; mywidth = 0.77 * 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 = 0.68 * 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>You can also download this PowerPoint at<br> </i></span></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.77 * 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>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><!-- -//--> -</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/slide0019_notes_pane.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019_notes_pane.htm deleted file mode 100755 index e2cb435a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0019_notes_pane.htm +++ /dev/null @@ -1,5 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 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=Verdana size=2>END</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/slide0020.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0020.htm deleted file mode 100755 index da8b9759..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0020.htm +++ /dev/null @@ -1,172 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); 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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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0 * g_width; myheight = 0.86 * g_height; mywidth = 0.86 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0 * g_width; -yy = 0.08 * g_height; -ht = 0.86 * g_height; -wd = 0.86 * g_width; -document.write( -'<img border=0 src="slide0002_image002.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.34 * g_height; myleft = 0.59 * 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 language=JavaScript><!-- -xx = 0.59 * g_width; -yy = 0.34 * g_height; -ht = 0.14 * g_height; -wd = 0.12 * g_width; -document.write( -'<img border=0 src="slide0002_image003.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.46 * g_height; myleft = 0.85 * 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 * g_width; myheight = 0.1 * 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 = 0.13 * g_width; - 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'>Choose<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 style='mso-line-spacing:"-224 0 0"'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>database</span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.62 * g_height; myleft = 0.86 * 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 = 0.18 * 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 = 0.05 * 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 = 0.18 * g_width; - 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> - mytop = 0.77 * g_height; myleft = 0.85 * g_width; myheight = 0.12 * 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 = 0.01 * 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> - 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 style='mso-line-spacing:"-224 0 0"'><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3'>search</span></div> </layer></div> </layer></div> </layer><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.09 * g_height; mywidth = 1.11 * 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 = 1.1 * 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 = 1.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 348;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>PART 1: How to study variation and covariation</span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.15 * g_height; myleft = 0.85 * g_width; myheight = 0.22 * g_height; mywidth = 0.16 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.21 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%;mso-line-spacing:"-224 0 0";mso-line-spacing:"-224 0 0"'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>Choose<span style="mso-spacerun: yes"> </span></span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>species, </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>group, </span></span></layer><script> - mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>and type</span></span></layer></div> </layer></div> </layer><script> - mytop = 0.71 * g_height; myleft = 0.48 * g_width; myheight = 0.13 * g_height; mywidth = 0.12 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.48 * g_width; -yy = 0.71 * g_height; -ht = 0.13 * g_height; -wd = 0.12 * g_width; -document.write( -'<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"> </span>http://www.genenetwork.org</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>To begin a search you make choices about what species, group, and database to explore.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>For this demonstration enter APP as above and click on the SEARCH button. Make sure that the DEFAULT SETTINGS are species = Mouse, Group = BXD, Type = Whole Brain, and Database = INIA BRAIN mRNA M430 (Apr05) PDNN.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. The GeneNetwork and WebQTL are often used to work with public data sets. However, it is possible to enter and analyze your own data for specific genetic reference populations such as the BXD genetic reference population of mice or the HXB strains of rat. Entering your own data is a more advanced topic, but if you click on the HOME pop-down menu (upper left), you will see ÒEnter Trait DataÓ that will explain the process.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>2.</font><font face=Helvetica size=3> For help on advanced searching methods read the left side of the page (INTRODUCTION).<span style="mso-spacerun: yes"> </span>If you make a search term too complex, you may get no hits (try entering Òamyloid betaÓ for example). If you make it too simple, you may also get too many.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>3.</font><font face=Helvetica size=3> Use the asterisk * as a wildcard. For example, to find all <i>Hoxb</i> transcripts, search for Hoxb*.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>4.</font><font face=Helvetica size=3> In some cases you can also research for transcripts and genes using special search strings such as Ò</font><font face=Geneva size=3>Mb = (Chr1, 100 102)Ó to find all genes on Chromosome 1 between 98 and 104 megabases (donÕt actually use the quotes). Details are described at </font><font face=Verdana size=3>http://www.genenetwork.org/searchHelp.html</font><font face=Geneva size=3>.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>5.<span style="mso-spacerun: yes"> </span>These INFO buttons provide links to data about the different data types. Try them.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>6.<span style="mso-spacerun: yes"> </span>The SET TO DEFAULT button is used to change the database default setting to match your typical search categories.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ 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 deleted file mode 100755 index 0e0eb529..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0021.htm +++ /dev/null @@ -1,129 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate 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: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("slide0021.htm"); -}//--> -</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> - -g_origHeight = 566; 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-</script> <div><script> - mytop = 0 * 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> <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 = 1.04 * 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'>Please also use the Glossary, FAQ, and News</span></div> </layer></div> </layer></div> </layer><script> - mytop = 0.1 * g_height; 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myleft = 0.38 * g_width; myheight = 0.48 * g_height; mywidth = 0.6 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.38 * g_width; -yy = 0.49 * g_height; -ht = 0.48 * g_height; -wd = 0.6 * g_width; -document.write( -'<img border=0 src="slide0003_image009.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>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() { - -} -//--> -</script> </body> </html> \ No newline at end of file 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 deleted file mode 100755 index 663a5f0f..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0022.htm +++ /dev/null @@ -1,140 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); 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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'>set in red </span></span></layer><script> - mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>and</span><span style='font-family:"Gill Sans"; font-size:217%;color:#E9EB5D;mso-color-index:3;display:none'><i><br> </i></span></span></layer></div> </layer><script> - mytop = 0.2 * g_height; myleft = 0 * g_width; myheight = 0.26 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-line-spacing:"-224 0 0"'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>click. You </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>do NOT </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>have to </span></span></layer><script> - mytop = 0.15 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>select the </span></span></layer><script> - mytop = 0.2 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.18 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:217%; color:#E9EB5D;mso-color-index:3'>checkbox</span><span style='font-family:"Gill Sans"; font-size:250%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> - mytop = -0.04 * g_height; myleft = 0.01 * 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 = 0.05 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * 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:82%'>Search results</span><span style='mso-special-format:lastCR;display:none'><br> </span></div> </layer></div> </layer></div> </LAYER> - <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>RESULTS OF THE APP SEARCH.<span style="mso-spacerun: yes"> </span>A search of the INIA Brain database generates 18 matches, 10 of which are shown above. The GeneNetwork will display several hundred matches in pages of 40 each. If a search generates a larger numbers of hits, then you will need to refine search terms.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>1. APP is a great transcript to introduce you to the complexity and power of new array platforms that often provide ÒalternativeÓ expression estimates for single genes. There are seven probe sets that target different parts of the APP transcript. Which of the alternative measurements is most appropriate and informative? Have a look at the FAQ page for more on this topic, but general advice: 1. be skeptical and try to validate that the correct transcript and gene is being measured; 2. check what part of the transcript is complementary to the probes; 3. evaluate the performance of individual probes based on expression level, signal-to-noise and other error terms such as the standard deviation and error.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. In this particular case we have highlighted and selected # 5 on this SEARCH RESULTS page. The annotation for this probe set mentions that it targets the last three exons and the 3Õ untranslated region (UTR) of the amyloid precursor protein (APP).<span style="mso-spacerun: yes"> </span>That is just what we want.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. Most probe sets have not been annotated in as much detail as App. Refer tot the FAQ to learn how to annotate probe sets yourself.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm deleted file mode 100755 index 10a6218a..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0023.htm +++ /dev/null @@ -1,128 +0,0 @@ -<html> <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: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("slide0023.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0.02 * g_width; myheight = 0.8 * g_height; mywidth = 0.77 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.02 * g_width; -yy = 0.08 * g_height; -ht = 0.8 * g_height; -wd = 0.77 * g_width; -document.write( -'<img border=0 src="slide0005_image013.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.01 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 1.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.06 * g_height; mywidth = 1.06 * 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: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> - mytop = 0.34 * g_height; myleft = 0.68 * 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 language=JavaScript><!-- -xx = 0.68 * g_width; -yy = 0.34 * g_height; -ht = 0.09 * g_height; -wd = 0.16 * g_width; -document.write( -'<img border=0 src="slide0005_image014.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.23 * g_height; myleft = 0.84 * g_width; myheight = 0.34 * 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 = 0.32 * 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 = 0.14 * 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'><i>Click </i></span></span></layer><script> - mytop = 0.05 * 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><span style='text-align:left'><span style='font-size:200%;color:#E9EB5D'><i>here<br> </i></span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.15 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><span style='font-size:200%;color:#E9EB5D'><i>to learn<br> </i></span></div> </layer><script> - mytop = 0.16 * 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><span style='font-size:200%;color:#E9EB5D'><i>about<br> </i></span></div> </layer><script> - mytop = 0.21 * 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><span style='font-size:200%;color:#E9EB5D'><i>data<br> </i></span></div> </layer><script> - mytop = 0.27 * 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><span style='font-size:200%;color:#E9EB5D'><i>source</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=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 deleted file mode 100755 index 97f09734..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0024.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html> <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: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("slide0024.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = -0.01 * 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><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.97 * 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'>Data sources: Metadata for each resource</span></div> </layer></div> </layer><script> - mytop = 0.06 * g_height; myleft = 0.03 * g_width; myheight = 0.92 * g_height; mywidth = 0.6 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.03 * g_width; -yy = 0.06 * g_height; -ht = 0.92 * g_height; -wd = 0.6 * g_width; -document.write( -'<img border=0 src="slide0006_image015.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>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> </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/slide0025.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0025.htm deleted file mode 100755 index 32820d64..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0025.htm +++ /dev/null @@ -1,134 +0,0 @@ -<html> <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: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("slide0025.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 1.09 * 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 = 0.06 * g_height; mywidth = 1.07 * 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: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> </layer></div> </layer><script> - mytop = 0.81 * g_height; myleft = 0.02 * g_width; myheight = 0.11 * g_height; mywidth = 1.1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.09 * 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 = 0.04 * g_height; mywidth = 1.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:183%; color:#E9EB5D;mso-color-index:3'>Trait data for each strain with SE when known. For array data the scale is </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.92 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:183%; color:#E9EB5D;mso-color-index:3'>~ log base 2.<span style="mso-spacerun: yes"> </span></span><span style='font-size:167%;color:#E9EB5D; mso-color-index:3'>F1 data = 16.723 = 2^16.723 = 108,174</span></span></layer></div> </layer></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0.02 * g_width; myheight = 0.72 * g_height; mywidth = 0.51 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.02 * g_width; -yy = 0.07 * g_height; -ht = 0.72 * g_height; -wd = 0.51 * g_width; -document.write( -'<img border=0 src="slide0007_image016.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.33 * g_height; myleft = 0.57 * g_width; myheight = 0.13 * g_height; mywidth = 0.3 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.57 * g_width; -yy = 0.33 * g_height; -ht = 0.13 * g_height; -wd = 0.3 * g_width; -document.write( -'<img border=0 src="slide0007_image017.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.47 * g_height; myleft = 0.57 * g_width; myheight = 0.18 * g_height; mywidth = 0.36 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.18 * g_height; mywidth = 0.35 * 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 = 0.04 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index: 3'>These values can all </span></span></layer><script> - mytop = 0.04 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index: 3'>be changed by the </span></span></layer><script> - mytop = 0.09 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.35 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index: 3'>user. (Yes, there is a </span></span></layer><script> - mytop = 0.13 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 0.33 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:167%;color:#E9EB5D;mso-color-index: 3'>RESET)</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=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> </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/slide0026.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0026.htm deleted file mode 100755 index 7dac49e1..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0026.htm +++ /dev/null @@ -1,130 +0,0 @@ -<html> <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: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("slide0026.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.08 * g_height; mywidth = 0.98 * 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:"-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'>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> </layer></div> </layer><script> - mytop = 0.74 * g_height; myleft = 0.02 * g_width; myheight = 0.13 * g_height; mywidth = 1.1 * 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 = 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 = 0.04 * 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:150%; color:#E9EB5D;mso-color-index:3'>Use the BASIC STATISTICS button to evaluate the App data. You will find that App data </span></span></layer><script> - mytop = 0.03 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.09 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:150%; color:#E9EB5D;mso-color-index:3'>from the different strains are not equally trustworthy. BXD8 is an obvious outlier without </span></span></layer><script> - mytop = 0.07 * g_height; myleft = 0 * g_width; myheight = 0.04 * g_height; mywidth = 1.03 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:150%; color:#E9EB5D;mso-color-index:3'>replication (no error bar)</span><span style='font-size:150%;color:#E9EB5D;mso-color-index:3'>. BXD33 is also suspiciously low. BXD5 is noisy. </span><span style='font-family:"Gill Sans"; font-size:150%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> - mytop = 0.07 * g_height; myleft = 0.02 * g_width; myheight = 0.18 * g_height; mywidth = 0.16 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.02 * g_width; -yy = 0.07 * g_height; -ht = 0.18 * g_height; -wd = 0.16 * g_width; -document.write( -'<img border=0 src="slide0008_image018.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0.18 * g_width; myheight = 0.66 * g_height; mywidth = 0.73 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.18 * g_width; -yy = 0.08 * g_height; -ht = 0.66 * g_height; -wd = 0.73 * g_width; -document.write( -'<img border=0 src="slide0008_image019.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.87 * g_height; myleft = 0.59 * g_width; myheight = 0.13 * g_height; mywidth = 0.3 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.59 * g_width; -yy = 0.87 * g_height; -ht = 0.13 * g_height; -wd = 0.3 * g_width; -document.write( -'<img border=0 src="slide0008_image021.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>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><!-- -//--> -</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/slide0027.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0027.htm deleted file mode 100755 index 0a23d59d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0027.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate 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: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("slide0027.htm"); -}//--> -</script> </head> <body onresize="restore()" onload="DoOnLoad()" style='font-size:&{font_size()};' bgcolor="#000000"> <script> - -g_origHeight = 566; -g_origWidth = 755; 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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 = 0.01 * 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 = 0.9 * 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'> expression after windsorizing</span></div> </layer></div> </layer><script> - mytop = 0.08 * g_height; myleft = 0.02 * g_width; myheight = 0.83 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.02 * g_width; -yy = 0.08 * g_height; -ht = 0.83 * g_height; -wd = 0.94 * g_width; -document.write( -'<img border=0 src="slide0009_image022.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>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> </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/slide0028.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0028.htm deleted file mode 100755 index cde4a136..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0028.htm +++ /dev/null @@ -1,104 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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: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("slide0028.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.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: 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'>Discovering shared expression patterns</span></div> </layer></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.03 * g_width; myheight = 0.37 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.03 * g_width; -yy = 0.1 * g_height; -ht = 0.37 * g_height; -wd = 0.94 * g_width; -document.write( -'<img border=0 src="slide0010_image023.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.38 * g_height; myleft = 0.61 * g_width; myheight = 0.14 * g_height; mywidth = 0.13 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.61 * g_width; -yy = 0.38 * g_height; -ht = 0.14 * g_height; -wd = 0.13 * g_width; -document.write( -'<img border=0 src="slide0010_image024.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>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><!-- -//--> -</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/slide0029.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0029.htm deleted file mode 100755 index c296b9e9..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0029.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate 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: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("slide0029.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.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 = 0.9 * 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'>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><!-- -xx = 0.02 * g_width; -yy = 0.07 * g_height; -ht = 0.91 * g_height; -wd = 0.85 * g_width; -document.write( -'<img border=0 src="slide0011_image025.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>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 deleted file mode 100755 index b84e4aad..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0030.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate 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: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("slide0030.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0 * g_height; myleft = 0.01 * 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 = 0.9 * 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> - mytop = 0.08 * g_height; myleft = 0.05 * g_width; myheight = 0.91 * g_height; mywidth = 0.66 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.05 * g_width; -yy = 0.08 * g_height; -ht = 0.91 * g_height; -wd = 0.66 * g_width; -document.write( -'<img border=0 src="slide0012_image026.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>By clicking on the CORRELATION of the Atcay transcript to the App transcript, you can generate a Correlation plot between these two transcripts. In this App and Atcay scatterplot, each point is a strain mean value. For example, BXD33 and BXD8 have low App and Atcay expressions. The two parental strains and the F1 are also included in this plot.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0031.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0031.htm deleted file mode 100755 index 9a54b689..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0031.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html> <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: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("slide0031.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.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> - mytop = 0.09 * g_height; myleft = 0.02 * g_width; myheight = 0.9 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.02 * g_width; -yy = 0.09 * g_height; -ht = 0.9 * g_height; -wd = 0.83 * g_width; -document.write( -'<img border=0 src="slide0013_image027.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>A group of traits from many different databases can be selected and brought together for joint analysis. In this case all of the content of the BXD SELECTIONS is from a single BRAIN database, the top 20 neighbors of the App transcript from the Correlation Results table. Eight of these neighbors plus App is shown in the slide.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>All of items in the BXD SELECTIONS were selected using the SELECT ALL button</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. The buttons at the top (and bottom) of this page can do some cool stuff. We will work with NETWORK GRAPH first.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>3. Think of the SELECTIONS as your shopping cart. You go to different aisles in the supermarket to acquire different types of items of interest. These could include transcripts, classical phenotypes (longevity, brain weight, prepulse inhibition, iron levels in midbrain). ÒChecking outÓ in this case involves doing some analysis with the items in the cart.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>4. Different tools handle different numbers of items. Most will handle up to 100 traits.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0032.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0032.htm deleted file mode 100755 index 85ee47fe..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0032.htm +++ /dev/null @@ -1,118 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: App transcript coexpression neighborhood"> <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("slide0032.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</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 + ' >' ); -</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> - mytop = 0.37 * g_height; myleft = 0.01 * g_width; myheight = 0.62 * g_height; mywidth = 0.97 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.01 * g_width; -yy = 0.37 * 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; -document.write( -'<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"> </span>Size of 16 by 16 inches; Gene Symbols; Don't Show Correlations; Use curved lines (aka ÒedgesÓ).</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm deleted file mode 100755 index 042ca4ad..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0033.htm +++ /dev/null @@ -1,104 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <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: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("slide0033.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.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> - mytop = 0.28 * g_height; myleft = 0.04 * g_width; myheight = 0.7 * g_height; mywidth = 0.78 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script language=JavaScript><!-- -xx = 0.04 * g_width; -yy = 0.28 * g_height; -ht = 0.7 * g_height; -wd = 0.78 * g_width; -document.write( -'<img border=0 src="slide0015_image034.png" x=' + xx + ' y=' +yy + ' height=' + ht + ' width=' + wd + '>' ); -//--> -</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; -yy = 0.08 * g_height; -ht = 0.19 * g_height; -wd = 0.33 * g_width; -document.write( -'<img border=0 src="slide0015_image035.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>Going back to the Trait Data and Analysis Form window, we have computed the correlations between strain variation in App expression level and other classical phenotypes that have already been measured in many of the same BXD strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>Notes:</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Arial size=3>1.</font><font face=Helvetica size=3>The number of common strains varies widely--in this case from 14 to 23 strains.</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>2. We can add these traits (four are selected) to our BXD SELECTIONS window.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!-- -//--> -</script><script language=JavaScript><!-- -function playList() { - -} -//--> -</script> </body> </html> \ No newline at end of file diff --git a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0034.htm b/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0034.htm deleted file mode 100755 index 3cf1ac70..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0034.htm +++ /dev/null @@ -1,93 +0,0 @@ -<html> <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: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("slide0034.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.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 deleted file mode 100755 index ca5ac8bb..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0035.htm +++ /dev/null @@ -1,151 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <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: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("slide0035.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</script></div> </layer><script> - mytop = 0.01 * g_height; myleft = 0.03 * g_width; myheight = 0.14 * g_height; mywidth = 0.93 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.07 * g_height; mywidth = 0.91 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0;mso-line-spacing:"-220 0 -216";mso-margin-left-alt: 292;mso-text-indent-alt:0'><span style='mso-special-format:nobullet;display: none;color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>Summary of Part 1:</span><span style='font-size:94%;color:#E9EB5D;mso-color-index:3;mso-special-format:lastCR; display:none'><br> </span></div> </layer></div> </layer><script> - mytop = 0.1 * g_height; myleft = 0.08 * g_width; myheight = 0.47 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <layer> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'></div> </layer> <script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.84%;font-family:Arial'>1.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You have learned the basics about searching for traits<br> </span></span></layer></div> </layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.85 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-3.03%;font-family:Arial'>2.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know some methods to check data quality<br> </span></span></layer></div> </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"> </span>You know how to edit bad or suspicious data<br> </span></span></layer></div> </layer><script> - mytop = 0.16 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 0.9 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.88 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.85%;font-family:Arial'>4.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to review the basic statistics of a trait<br> </span></span></layer></div> </layer><script> - mytop = 0.21 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 0.94 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.91 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.74%;font-family:Arial'>5.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a scattergram between two </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>traits using the Traits Correlation tool<br> </span></span></layer></div> </layer><script> - mytop = 0.31 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; 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 + ' >' ); -</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:-2.56%;font-family:Arial'>6.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to add items to your SELECTIONS window<br> </span></span></layer></div> </layer><script> - mytop = 0.37 * g_height; myleft = 0 * g_width; myheight = 0.1 * g_height; mywidth = 1 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='mso-special-format:numbullet;font-family:Arial;text-align:left; font-family:Verdana;font-weight:normal;font-style:normal;text-decoration:none; text-shadow:none;text-effect:none;mso-fareast-hint:no;layout-flow:horizontal; color:black;mso-color-index:1;font-size:80%;mso-text-raise:0%;mso-margin-left-alt: 144;mso-margin-left-alt:144'><script> - mytop = 0 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.97 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'><span style='mso-special-format:numbullet; position:absolute;left:-2.57%;font-family:Arial'>7.</span></span><span style='font-family:"Gill Sans";font-size:200%;color:#E9EB5D;mso-color-index: 3'><span style="mso-spacerun: yes"> </span>You know how to generate a Network Graph of traits that </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0.02 * g_width; myheight = 0.05 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>co-vary. </span></span></layer></div> </layer></div> </layer><script> - mytop = 0.67 * g_height; myleft = 0.05 * g_width; myheight = 0.26 * g_height; mywidth = 1.05 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.05 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>What does genetic covariance mean? The genetic covariance can </span></span></layer><script> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D;mso-color-index:3'>be functional and mechanistic, but it can also be due to linkage </span></span></layer><script> - mytop = 0.1 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.01 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; 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 deleted file mode 100755 index ccec2e7d..00000000 --- a/web/tutorial/ppt/html/webqtl_demo2_part1.ppt_files/slide0036.htm +++ /dev/null @@ -1,112 +0,0 @@ -<html> <head> <meta name=ProgId content=PowerPoint.Slide> <meta name=Generator content="Microsoft Macintosh PowerPoint 11"> <title>PowerPoint Presentation - Complex trait analysis, develop-ment, and genomics</title> <link title="Presentation File" type="application/powerpoint" rel=alternate href="webqtl_demo2_part1.ppt.ppt"> <script> -if ( ! top.PPTPRESENTATION ) { - window.location.replace( "endshow.htm" ); -} -</script> <meta name=Description content="Aug-15-05: 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() { - 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("slide0036.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.png" height=' + ht + ' width=' + wd + '>' ); -//--> -</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; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div><script> - mytop = 0 * g_height; myleft = 0.01 * g_width; myheight = 0.24 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:"Gill Sans";font-weight:normal; font-style:normal;text-decoration:none;text-shadow:none;text-effect:none; mso-fareast-hint:no;layout-flow:horizontal;color:#E9EB5D;font-size:293%; mso-text-raise:0%;mso-line-spacing:"-358 0 -1";mso-line-spacing:"-358 0 -1"'><script> - mytop = 0 * g_height; myleft = 0 * g_width; myheight = 0.07 * g_height; mywidth = 0.87 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:82%'>rwilliam@nb.utmem.edu<br> </span></span></layer><script> - mytop = 0.08 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:82%'><br> </span></span></layer><script> - mytop = 0.16 * g_height; myleft = 0.04 * g_width; myheight = 0.07 * g_height; mywidth = 0.83 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-size:82%;mso-special-format:lastCR; display:none'><br> </span></span></layer></div> </layer></div> </layer><script> - mytop = 0.27 * g_height; myleft = 0.09 * g_width; myheight = 0.07 * g_height; mywidth = 0.5 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script> <div style='text-align:left;font-family:Verdana;font-weight:normal;font-style: normal;text-decoration:none;text-shadow:none;text-effect:none;mso-fareast-hint: no;layout-flow:horizontal;color:black;mso-color-index:1;font-size:80%; mso-text-raise:0%'><span style='font-family:"Gill Sans";font-size:300%; color:#E9EB5D'>kmanly@utmem.edu</span></div> </layer><script> - mytop = 0.83 * g_height; myleft = 0.04 * g_width; myheight = 0.15 * 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> - mytop = 0.05 * g_height; myleft = 0 * g_width; myheight = 0.05 * g_height; mywidth = 1.08 * g_width; - document.write( '<layer top=' + mytop + ' left=' + myleft + ' height=' + myheight + ' width=' + mywidth + ' >' ); -</script><span style='text-align:left'><span style='font-family:"Gill Sans";font-size:200%; color:#E9EB5D'>ongoing study by R. Williams. R. Homayouni, and R. 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