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Genes must be polymorphic
to generate downstream genetic effects (as opposed to downstream molecular
effects). Hars2 meets this condition because we have already mapped a
functional polymorphism in the gene. We can therefore posit that Hars2 is a
QT gene. What transcripts are downstream? App is one obvious
candidate, but there are many more.
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The are several ways to
look for downstream targets. The best and most obvious is to look up all
transcripts that have high correlations with Hars2 itself. You should know
how to do this. An alternative method is shown here for teaching purpose and
to show you what to do if your gene of interest is not in our database. You
need to know:
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1. Where your gene is located. You need this information
to find a surrogate marker; a marker that is located very close to your gene
of interest.
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2. That your gene is
polymorphic between C57BL/6J and DBA/2J.
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LetÕs look at the
correlation of Hars2 with BXD genotypes as shown in the slide above to
illustrate how to use markers as surrogate traits.
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Go to the Trait Date and
Editing window one more time. We want the data for Hars2 this time, not App.
You should be able to show that Hars2 has a high correlation with D2Mit423 as shown in the slide above.
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By clicking on the symbol
D2Mit423 in the Correlation window, you will generate a new Trait Data
window shown on the next slide.
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