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.    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.


GenIndexer Testing


·     Go to http://shad.cs.utk.edu/cgx

·     Login: Username ‘guest’, password ‘guest1’

·     Select LL-Mouse-homol document collection from the pull-down menu.


1)    Select the saved query ‘Class Assignment’ and 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)    Examine the Hierarchical tree structure in GeneIndexer for the 50_TestGene collection.

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.



STRING Testing


·     Go to http://string.embl.de/


1) Perform a multi-gene query

o     Take the top 5 genes from GeneIndexer output on Reelin query 

o     Perform a multiple gene query in STRING

o     Examine the network structure. Which gene/proteins are experimentally shown to interact and which interactions are implied through text mining

2) Perform a single-gene query for Dab1

o     Compare these results to those from GeneIndexer and iHOP above

o     Add an additional 5 ‘white nodes’ to the graph and compare these results to GeneIndexer results.