iHOP
Testing
·
Go to http://www.ihop-net.org/
·
Search
for the mouse gene name Reln using the search utility at the bottom of the
page.
1)
Click
on the ‘interaction information for this gene’ icon on the right hand side of
the results and then wait until the page finishes loading. Now, Click on the
“show overview link in the left hand side.
a.
What
is the nearest neighbor of Reln?
b.
How
many sentences are in common between Reln and the nearest neighbor?
c.
Why
are there multiple symbols for the same gene in the list of interactions?
d.
Do you
see an association between Reln and APP or APLP1 in this list? Explain why or
why not.
2)
Click
on the gene symbol Dab1 and then click on the “show overview link in the left
hand side in the following page.
a.
What
is the nearest neighbor of Dab1?
b.
Do you
see an association between Dab1 and APP or APLP1 in this list? Explain where
and why.
SGO Testing
·
Go to http://shad.cs.utk.edu/sgo
·
Login
as anonymous user
·
IMPORTANT:
Leave the session name field empty.
1)
Perform
a keyword query using ‘reelin’, ‘dab1’ and ‘VLDLR’
a.
What
are the top 5 ranked genes and their corresponding scores returned by the
query?
b.
Does
this fit the known biology?
c.
Considering
the Reelin signaling diagram in the lecture, what are some indirect gene
relationships to Reln and their corresponding rank score?
2)
Perform
an accession number query using AV263736, Y08380, L33417.
a.
What
are the top 5 ranked genes and their corresponding scores returned by the
query?
b.
Does
this fit the known biology (Reelin signaling pathway components)?
c.
What
are some indirect gene relationships to Reln and their corresponding
rank score?
BONUS: What
is the major difference in the rank scores of the accession query and keyword
query. Why?
3)
Examine
the Hierarchical tree structure using the ATV (A Tree Viewer) feature.
a.
Identify
the Reln cluster. Does this fit into the known signaling pathway?
b.
Name
at least 1 more cluster of genes which contains at least 3-6 genes.
4)
Examine
the graphical structure of the 50 gene collection using the Nodal tree feature.
a.
The
threshold for the relationship distance between genes is set to 0.7 (1-cosine
of the vector angle). Why is the cdk5 cluster of genes separated from the main
graph?
b.
Identify
the Reln cluster of genes. Does this fit the known biology?