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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD><TITLE>QTL heatmap</TITLE>
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<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>
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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.
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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.
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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).
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