- Course overview
- Search within this course
- Network analysis in biology
- Introduction to graph theory
- Types of biological networks
- The sources of data underlying biological networks
- Building and analysing PPINs
- Summary
- Quiz: Check your learning
- Your feedback
- Learn more
- References
Properties of PPINs: scale-free networks
Protein-protein interaction networks are scale-free networks (Figure 18A). The majority of nodes (proteins) in scale-free networks have only a few connections to other nodes, whereas some nodes (hubs) are connected to many other nodes in the network.
![](https://www.ebi.ac.uk/training/online/courses/network-analysis-of-protein-interaction-data-an-introduction/wp-content/uploads/sites/64/2020/08/new-fig-18-1024x638.png)
The number of connections each node has is called its degree. If we represent the degree distribution of a scale-free network in a logarithmic scale, we can see how it fits with a line (they fit a power-law), having a small number of nodes with high degree (the hubs) and a large number of nodes with a low degree (Figure 18B).
Scale-free networks can be built following the preferential attachment model, also known as the ‘rich get richer’ principle. This principle simply states that scale-free networks can be built by adding edges that are preferentially attached to those nodes with a highest degree (5). This building principle provides a self-organising mechanism for the generation and expansion of this type of network.
The scale-free nature of protein-protein interaction networks gives them a number of important features:
- Stability
- If failures occur at random, and the vast majority of proteins are those with a small degree of connectivity, the likelihood that a hub would be affected is small
- If a hub-failure occurs, the network will generally not lose its connectedness, due to the remaining hubs
- Invariant to changes of scale
- No matter how many nodes or edges the network has, its properties remain stable
- The presence of hubs is what allows for the small-world effect to be present regardless of the size of the network
- Vulnerable to targeted attack
- If we lose a few major hubs from the network, the network is turned into a set of rather isolated graphs
- Hubs are enriched with essential/lethal genes. For example, many cancer-linked proteins are hub proteins (e.g. the tumour suppressor protein p53)
![]() |