Boolean_Algebra
The Boolean Algebra Tools preforms a Union, Intersection, or
Exception on at least two GeneSets. It then provides a listing of
genes grouped by the number of GeneSets they have in common. This
view may allow you to quickly determine new relationships between
GeneSets and create a new GeneSet based on your findings.
The Union of two or more GeneSets is defined as every gene which is
in any of the sets. For example, if GeneSet A = {2,4,5,6} and
GeneSet B = {1,2,3} then A U B = {1, 2, 3, 4, 5, 6}. The Boolean
Algebra tool will return all the genes in the selected GeneSets and
indicate the GeneSet(s) it is found in.
The Intersection of two sets A and B is defined as the set that
contains all elements of A that also belong to B (or all elements
of B that also belong to A), but no other elements. The Boolean
Algebra tool will return all combinations of intersections for the
selected GeneSets. Section headings on the results indicate how
many GeneSets the gene has in common. For example, say there are
three GeneSets, and A = {1, 2}, B = {1, 3}, and C = {1, 3}. The
Boolean Algebra Tool will not only return the results that A ? B ?
C = {1}, it will also return the intersection of B and C which is
equal to 3.
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The red shaded areas in the figure to the right represent the
results which would be returned from the Boolean Algebra tool for
an Intersection operation on three GeneSets.
The third set logic operation the Boolean Algebra tool provides is
Except, sometimes also referred to as Minus or Complement. For
example, if GeneSet A = {1,2} and GeneSet B = {2,3}, A minus B
would be {1}. For the Boolean Algebra’s tools purposes, the list of
genes that is returned will be those which are only found uniquely
in one GeneSet. For example, if A = {1}. B = {1, 2}, and C = { 2,
4, 5}, the tool will return the following genes: 4, and 5.
The red shaded areas in the figure to the right represent the
results which would be returned from the Boolean Algebra tool for
an Exception operation on three GeneSets.
Access the Boolean Algebra Tool through the Analyze Genesets tab
under the Analyze Genesets option.
From the "Analyze Genesets" tab, select "Analyze Genesets". To
generate Boolean Algebra results, you must first select at least
two GeneSets from a project. Projects may be created and updated by
uploading GeneSets, searching the GeneWeaver database, or through
the use of other tools in the GeneWeaver System. Please see the
documentation for uploading GeneSets, Search, or Manage GeneSets to
learn more about these functions. On this page, all the GeneSets in
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a particular project can be selected by clicking the check box to
the left of the project’s name. Also, individual GeneSets in a
project can be selected by expanding the project by clicking on the
project’s name and then clicking the check boxes for individual
GeneSets within a project. Either option is valid, but at least two
GeneSets need to be selected to run the Boolean Algebra tool. After
that, select the "Boolean Algebra" from the Analysis Tools box.
This tool box is located to the left of your projects. After this
selection, three radio buttons will appear. Please select "Union",
"Intersection", or "Except" depending on the results you wish to
run. Then, press the run button.
Figure 1: After the GeneSets have been selected, select "Boolean Algebra"
from from the Analysis Tools box.
After the tool runs, you will be redirect to your results page.
The results are separated out based on the number of GeneSets the
gene was found in for the particular set operation in decreasing
order. For example in Figure 2 below, a union on a three GeneSets
was performed. There was not a gene found in common with all three
GeneSets, but there was a gene found in common with two of the
GeneSets. This result is displayed first, and the GeneSets it was
found in is displayed in the "In Gene Sets" column in the results
table.
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Figure 2: Example of Union Boolean Algebra results.
For each gene, links are provided to direct you to different
websites to learn more information about the particular gene.
These links can be found under the "Linkouts" column in the table.
By using the toggle switch under the "Emphasis" column in the
table, you can give emphasis to a particular gene. This will allow
it to show up more prominently as you use other GeneWeaver
features. Based on your findings, you can also select genes to
form a new GeneSet. This can be accomplished by checking the check
box located on the far right of each gene’s row. Once all of your
desired genes to add to your new GeneSet are selected, press the
orange "Add to New GeneSet" button location on the top of this
page. This will redirect you to the Upload GeneSet form page where
a few fields will be auto-populated for you. Most notably, the
Gene List under Gene Information on the bottom of the form will be
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filled out with each gene’s identifier and value. Please read the
this link [2] more information about uploading a new GeneSet into
GeneWeaver.
Figure 3: Gene List box from Upload GeneSet form.
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