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the Mouse Strain Comparison application
Requirements:
One of
-
Firefox 3.0 or Greater
-
Internet Explorer 7 or Greater
and JavaScript must be enabled (this is typically the default setting
for Firefox and Internet Explorer).
Overview:
Using this application in the simplest possible way you can determine
which genomic intervals are either a match or a miss-match between two
selected strains. Beyond that you can build a more complicated
expression by AND'ing and OR'ing the pairwise strain comparisons
together. For example if I want to see all of the interval where
B6 matches C3H, but where both of these are different from NZO I would
create an expression like:
(B6 = C3H) AND (B6 ≠ NZO). Note that
because of the equivalence constraint on B6 and C3H the expression
(B6 = C3H) AND (C3H ≠ NZO)
will give the same exact results.
Genome Selection:
The genome data that we currently have available is the imputed SNP
dataset that is available from the CGD data site.
Defining Equivalence:
The most important thing to keep in mind when you are defining the
equivalence parameters for strains is that unequal intervals are just
the inverse of equivalent intervals. What this means is that when you specify
that 10 SNPs in a row must match before an interval is defined as
"equivalent" that guarantees that every interval returned by the
expression
(B6 = C3H)
will span at least 10 SNPs, but it does not mean that every interval
returned by
(B6 ≠ C3H)
will span 10 SNPs . In fact they can be single SNP intervals!
Building the Expression:
The expression builder lets you create boolean strain comparison
expressions by AND'ing and OR'ing together pairwise strain expressions.
You can insert new pairwise expressions by clicking the (+) button or
remove them by clicking on the (-) button. You can also use the
drop-down options to change the strains being compared, the relationship
you are looking for (= or ≠) and whether a given row will be AND'd or
OR'd with the next pairwise expression.
Let us take a look at an example of how this can be used. If you have
four "high" strains (ie. have high values for a phenotype of interest)
named "A", "B", "C" and "D" and you have three low strains named
"X", "Y" and "Z", you may want to examine the regions where all
the high strains match, all of the low strains match AND none of the
high strains match the low strains. We can test this relationship
with the following expression:
(A=B) AND (A=C) AND (A=D) AND (X=Y) AND (X=Z) AND (X≠A)
The Graph:
The graph has a "refresh" button that allows you to update the graph
whenever parameters have been modified. This button is only enabled
if there are changes that have not yet been applied to the graph. There
is also a "busy indicator" that lets you know whether or not the
graph is being updated. If you want to save the graph you should be
able to right click on it for download.
Data:
The data links allow you to download a comma-seperated files which
contain all of the intervals that were specified. You can either
download the entire genome at once, or a single chromosome at a time.
Note that these files can be used directly as input for
the Genome Interval Overlap Calculator.
