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5.3
Exercises for Chap. 5
It is useful to repeat these tasks in Chap. 7.
This part of the exercise will focus on bioinformatic models in order to better under
stand possible system effects and the organism as a whole. A bioinformatic model can
provide various information about the network topology, e.g. a Boolean model about the
logical interconnection of the signaling components (e.g. activation, inhibition,
feedback/feedforward regulation) or a kinetic model about metabolic pathways, but also
predict the resulting network behavior. Bioinformatics models can answer any number of
questions. Usually, the function of the signaling cascade and how it can be used therapeuti
cally is of particular interest.
Task 5.1
The basis for a bioinformatics model includes interactions, such as protein-protein interac
tions. You can find these in various databases and thus generate a corresponding signal
network.
Which of the following statements are correct (multiple answers possible)?
A. The STRING database provides little information on protein-protein interactions.
B. One of the things I find in the PlateletWeb database is protein-protein interactions
in platelets.
C. In the KEGG, iHOP and HPRD database I find protein-protein interactions.
D. Signaling cascades are, in this sense, a type of protein-protein interaction.
E. Proteins can interact with each other directly or as complexes.
Task 5.2
Name and describe databases/software where you can get information about interaction
partners, e.g. of proteins.
Task 5.3
Explain how to bioinformatically screen a protein for potential interaction partners (name
and briefly describe two software/databases). What do they output in each case? What are
the advantages of comparing several software/databases with each other?
Task 5.4
An interaction database is the STRING server. What is the difference to other databases,
such as PlateletWeb or HPRD?
Task 5.5
Explain how to create a protein-protein interaction network.
5 Systems Biology Helps to Discover Causes of Disease