<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <HTML><HEAD><TITLE>QTL heatmap</TITLE> <META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> <LINK REL="stylesheet" TYPE="text/css" HREF='css/general.css'> <LINK REL="stylesheet" TYPE="text/css" HREF='css/menu.css'> <SCRIPT SRC="javascript/webqtl.js"></SCRIPT> </HEAD> <BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> <TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> <TBODY> <TR> <script language="JavaScript" src="/javascript/header.js"></script> </TR> <TR> <TD bgColor=#eeeeee class="solidBorder"> <Table width= "100%" cellSpacing=0 cellPadding=5><TR> <!-- Body Start from Here --> <TD valign="top" height="200" width="100%" bgcolor="#eeeeee"> <P class="title">What is QTL heatmap? <A HREF="/webqtl/main.py?FormID=editHtml"><img src="images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P> <Blockquote> The upper part of this page includes a hierarchical cluster tree of the set of traits you selected in the previous window. To generate this plot, we initially compute distances between pairs of traits using (1 - r) where r is the Pearson product-moment correlation. The hierarchy is assembled by successively linking traits and groups of traits. <P></P> The lower part of this page provides a QTL heat map for all members of the Cluster Tree, extending from proximal Chr 1 at the top to distal Chr X at the bottom. Each vertical column or stripe encodes the genome-wide p value computed on the basis of 1000 permutations. Orange triangles mark the approximate location of genes. <P></P> These QTL heat maps can be redrawn using alternative color assignments using the "Redraw Cluster Tree" option. The default heat map is "Grey + Blue + Red" in which more intense colors mark chromosomal regions with comparatively high linkage statistics and the spectrum encodes the allelic effect. For example, blue-green regions are those in which one of the parental alleles (e.g., C57BL/6J) is associated with higher trait values, whereas red-yellow regions are those in which the other parental allele is associated with higher trait values. Grey and black regions have insignfiicant linkage to trait variance. The "Blue + Red" option is similar but the entire genome is encoded for allele polarity, including regions without significant linkage. Finally, " Single Spectrum" provides a plot that does not distinguish between allelic effects and encodes the p values, ranging from insignificant (dark blue) to genome-wide significant (bright red). <P></P> </Blockquote> <P></P> </TD> </TR></TABLE> </TD> </TR> <TR> <TD align=center bgColor=#ddddff class="solidBorder"> <!--Start of footer--> <TABLE width="90%"> <script language='JavaScript' src='/javascript/footer.js'></script> </TABLE> <!--End of footer--> </TD> </TR> </TABLE> <!-- /Footer --> <script language="JavaScript" src="/javascript/menu_new.js"></script> <script language="JavaScript" src="/javascript/menu_items.js"></script> <script language="JavaScript" src="/javascript/menu_tpl.js"></script> <script language="JavaScript"> <!--// new menu (MENU_ITEMS, MENU_POS); //--> </script> <script src="http://www.google-analytics.com/urchin.js" type="text/javascript"> </script> <script type="text/javascript"> _uacct = "UA-3782271-1"; urchinTracker(); </script> </BODY> </HTML>