What is a PPI network?

The protein-protein interaction (PPI) network of an organism serves as a skeleton for its signaling circuitry, which mediates cellular response to environmental and genetic cues. Understanding this circuitry could improve the prediction of gene function and cellular behavior in response to diverse signals.

What is a PPI module?

A PPI module represents a group of proteins taking part in specific, separable functions such as protein complexes, metabolic pathways or signal transduction systems.

What is an interaction network?

Interaction networks deal with objects and the relations between them. An object-centric model learns the behaviour of individual objects and the aggregated effects of the interactions they participate in. A relation-centric model learns the behaviours of two or more interacting objects.

Are Protein-Protein Interactions directional?

For proteins protein 1 (p1) and protein 2 (p2), if a signal can flow in only one direction, for example from p1 to p2, the direction is ‘uni-directional’. On the other hand, if the signal can flow in both directions depending on a context, the direction is ‘bi-directional’.

How do you study Protein-Protein Interaction?

Characterizing protein–protein interactions through methods such as co-immunoprecipitation (co-IP), pull-down assays, crosslinking, label transfer, and far–western blot analysis is critical to understand protein function and the biology of the cell.

What are hub genes?

Hub genes are defined as genes with high correlation in candidate modules. High connectivity means that the connectivity ranked at top 10\%. For example, if the module size was 1000, then the genes with top 100 were defined as the hub genes.

What are the different types of gene interactions?

There are 8 main different types of gene interaction:

• The interaction between Dominant factors.
• Complementary factors.
• Supplementary factor.
• Epistasis.
• Effect of Inhibitory factor.
• Duplicate factors.
• Multiple factors or Polygenic Inheritance.
• Lethal factor.

What are the different types of protein protein interactions?

Protein-protein relationships are often the result of multiple types of interactions or are deduced from different approaches, including co-localization, direct interaction, suppressive genetic interaction, additive genetic interaction, physical association, and other associations.

How can you tell a protein complex?

Studying protein complexes is a technically challenging and time-consuming task. The most common experimental approaches used to identify protein complexes rely on the classical yeast two-hybrid (Y2H) system or affinity purification in combination with mass spectrometry (AP-MS).