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A. Network contains 11 nodes and 18 edges.

B. Network contains 18 nodes and 11 edges.

C. Network contains 1 nodes and 8 edges.

D. Network contains 8 nodes and 1 edges.

E. Network contains 111 nodes and 181 edges.

Task 5.9

Example:

Now your actual network analysis begins. For this, Cytoscape has numerous plugins to

choose from, such as the Biological Networks Gene Ontology Tool (BiNGO). Please

briefly inform yourself about Cytoscape (https://cytoscape.org/) or Plugin → Manage

Plugins – Search BiNGO (you can also download the current BiNGO version here). Now

perform a BiNGO search for all proteins of the network (Plugins → Start BiNGO 2.44;

please use the preset default parameters, but use Homo sapiens as organism).

Which of the following statements are correct (multiple answers possible)?

A. The BiNGO analysis identifies relatively few biological processes (less than 20).

B. In addition to the functions, the BiNGO analysis also shows me the p-value and

which genes are involved.

C. For example, the BiNGO analysis shows me the biological process cell cycle

checkpoint (GO-ID 75) with a BRCA1 involvement.

D. The BiNGO analysis identifies the biological process induction of apoptosis (GO-

ID 6917) as significant (p-value < 0.05), but also that all proteins of the network are

involved.

Task 5.10

Describe what a Gene Ontology is and how the GO terms are organized.

Task 5.11

Example:

Now take a look at the network topology. Please use the NetworkAnalyzer plugin for

this. Please also inform yourself about this beforehand via Cytoscape (https://cytoscape.

org/) or via Plugin → Manage Plugins – Search NetworkAnalyzer. Here you can also

download the current NetworkAnalyzer version. Now perform an analysis (Plugins →

NetworkAnalysis → AnalyzeNetwork → Treat the network as undirected) and familiarize

yourself with the various parameters and plots (then use, for example, “Parameter average

number of neighbors” and “Plot Node Degree Distribution”).

Which of the following statements are correct (multiple answers possible)?

5  Systems Biology Helps to Discover Causes of Disease