<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; 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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>