Interference is a Cytoscape plug-in for virtual experimental network topological analysis allowing virtual knock-out experiments on complex networks.
Centrality indexes allow categorizing nodes in complex networks according to their topological relevance (see CentiScaPe plugin). In a node-oriented perspective, centralities are very useful topological parameters to compute in order to quantify the effect of individual node(s) alteration. We have introduced the notion of interference and developed the Cytoscape plugin Interference to evaluate the topological effects of single or multiple nodes removal from a network. In this perspective, interference allows virtual node knock-out experiments: it is possible to remove one or more nodes from a network and analyze the consequences on network structure, by looking to the variations of the node centralities values. As the centrality value of a node is strictly dependent on the network structure and on the properties of other nodes in the network, the consequences of a node deletion are well captured by the variation on the centrality values of all the other nodes.
### Potential Applications
The interference approach can model common situations where real nodes are removed or added from/to a physical network:
- Biological networks, where one or more nodes (genes, proteins, metabolites) are possibly removed from the network because of gene deletion, pharmacological treatment or protein degradation. Interference can be used to:
- Simulate pharmacological treatment: one can potentially predict side effects of the drug by looking at topological properties of nodes in a drug-treated network, meaning with that a network in which a drug-targeted node (protein) was removed. To inhibit a protein (for instance a kinases) corresponds to removing the node from the network
- Simulate gene deletion: gene deletion implies losing encoded proteins, thus resulting in the corresponding removal of one or more nodes from a protein network
- Social and financial networks, where the structure of the network is naturally modified over time
- Power grid failures
- Traffic jam or work in progress in a road network
- Temporary closure of an airport in an airline network