Hub and bottleneck genes

Given a list of genes, identify all the interacting genes and the druggabilities of these interactions.

Template: Gene list -> Compounds that target hub or bottleneck genes

Template: Gene list -> Compounds that target hub or bottleneck genes

Hub is defined as the top 10% of the nodes in the high-confidence protein interactome ranked by node degree (the number of interactions that are associated with a given node).

Bottleneck is defined as the top 10% of the nodes in the high-confidence protein interactome ranked by betweenness centrality (the fraction of all the shortest paths in an interactome that pass through a given node).

The process how TargetMine identifies hubs and bottlenecks.

The process how TargetMine identifies hubs and bottlenecks.

High-confidence PPI here implies that the interaction was validated by more than 2 experiment methods or reported by more than 2 publications.

Check the references for the application and more details.

References:

  • Tripathi LP, et al. (2013) Understanding the Biological Context of NS5A-Host Interactions in HCV Infection: A Network-Based Approach. J Proteome Res. [PubMed:23682656]
  • Betweenness centrality is an indicator of a node’s centrality in a network. It is equal to the number of shortest paths from all vertices to all others that pass through that node. [Wikipedia: Betweenness centrality]