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Task 5.6

Example:

We want to take a closer look at protein-protein interactions and turn to network analy­

sis and modelling of regulatory networks. You now have the opportunity to generate a

network and then examine it for its biological function, for example, to detect well-­

connected proteins in a network, so-called hub proteins. Please note that for training pur­

poses we have only chosen a small network around BRCA1 (BReast CAncer 1, also

known as breast cancer gene 1). Normally, however, the network to be investigated is

always much larger and more complex, which makes a comprehensive network analysis

necessary.

Now search for all human interaction partners of BRCA1 from the string database

(https://string-­db.org/). Which of the following statements are correct (multiple answers

possible)?

A. The interaction of BRCA1 and ESR1 was found experimentally and has a very low

score (close to 0).

B. For the interaction of BRCA1 and ESR1 I get a high score (>0.99).

C. Each indicated interaction for BRCA1 was simultaneously found and predicted

experimentally.

D. All indicated interactions with a score >0.99 were found experimentally.

Task 5.7

Describe a simple method for creating an interaction network and analyzing it for function.

Task 5.8

Example:

Now download all human interaction partners of BRCA1 from the string database

(https://string-­db.org/). Please use the parameter “Experiments” (i.e. only all experimental

interactions) and a “confidence score” of 0.9. Save the network (under “save” as text sum­

mary; TXT – simple tab delimited flatfile).

Now that you have downloaded all experimentally determined interaction partners, you

can visualize and further analyze your small network. For this purpose, please inform

yourself about the software Cytoscape (https://cytoscape.org/) and download the free ver­

sion 2.8.3. To make sure that the interactions match, please compare your network with the

one in the solution section and please adjust it accordingly. Please save your network (cur­

rently still as .txt) also as .sif (simple interaction file), because Cytoscape needs this for­

mat. Now you just have to import your created interaction file BRCA1.sif into Cytoscape

via File → Import Network (Multiple File Type) and you are ready to go.

Which of the following statements will you see after loading the BRCA1.sif file?

5.3  Exercises for Chap. 5