Interference:

A tool for virtual experimental network topological analysis  

 

Authors: Giovanni Scardoni and Carlo Laudanna

 

Download Interference here

A Cytoscape plug-in for 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 the 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

How Interference plugin works

The Interference plug-in allows you identifying the area of influence of single nodes or group of nodes. Specifically, Interference:

  • Compute the centralities value of the network
  • Remove the node(s) of interest
  • Recompute the centralities in the new network (the one where the node(s) have been removed)
  • Evaluate the differences between the centralities in the two networks.

This allows identifying the differences between the two networks: the one with the node(s) of interest still present and the one where the node(s) have been removed. Some nodes will increase, whereas others will reduce, their individual centrality values. This may suggest hints on the functional, regulatory, relevance of specific node(s).

Positive Interference

If a node (A), upon removal from the network of a specific node (B) or of a group of nodes, decreases its value for a certain centrality index, its interference value is positive. This means that this node (A), topologically speaking, takes advantage (is positively influenced) by the presence in the network of the node (B) or of that group of nodes. Thus, “removal” of node (B) or of that group of nodes from the network, negatively affects the topological role of the node (A). This is called positive interference.

Negative Interference

If a node (A), upon removal from the network of a specific node (B) or of a group of nodes, increases its value for a certain centrality index, its interference value is positive. This means that this node (A), topologically speaking, is disadvantaged (is negatively influenced) by the presence in the network of the node (B) or of that group the nodes. Thus, “removal” of node (B) or of that group of nodes from the network, positively affects the topological role of node (A). This is called negative interference.

Examples and definition: to better understand the meaning of interference, see the Examples and the Interference Tutorial.

Interference is a Centralities based measure

Interference plug-in computes the Interference values for the following centralities:

  • Eccentricity
  • Closeness
  • Betweenness
  • Stress
  • Centroid
  • Radiality

Several kind of graphical outputs

Interference supports several different graphical outputs:

  • Heat Map of interference results

  • Plot by centrality: Identify the nodes with high interference values and integrate the analysis with biological attributes from lab experiment.
  • Plot by node: Analyze single node interference values
  • Boolean highlight: Highlight nodes by their interference values

More about Interference

Contacts

  • If you have any question about Interference please do not hesitate to contact us:

    giovanni.scardoni(at)gmail.com

 


Download Interference here